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finswimmer ♦ 11k
Role: Moderator
Status: New
Handle: @finswimmer37605
Reputation: 11100
Email: f*********@gmail.com
Joined: 17 months ago
Last seen: 9 months ago
Location: Germany

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Comment: C: No reads in IGV at the positions indicated by the bed file
17 months ago
finswimmer 11k
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168
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Answer: A: tabix to exclude chromosomes from vcf
17 months ago
finswimmer 11k
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124
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Comment: C: snpEff for bacteria genome
17 months ago
finswimmer 11k
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Answer: C: Exclude sites on the basis of the proportion of missing data using BCFTOOLS
17 months ago
finswimmer 11k
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Comment: C: Available tools that can pick up the the alignment with highest mapping quality
17 months ago
finswimmer 11k
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Answer: A: samtools SNP calling
18 months ago
finswimmer 11k
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Comment: C: Any database can substitute OMIM?
18 months ago
finswimmer 11k
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Comment: C: Replacing missing SNPs of one individual with reference alleles in a vcf file
18 months ago
finswimmer 11k
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143
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Answer: A: awk to organize bed file
18 months ago
finswimmer 11k
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Comment: C: get consensus sequence from bam file with insertions
18 months ago
finswimmer 11k
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163
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Comment: C: get consensus sequence from bam file with insertions
18 months ago
finswimmer 11k
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144
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Comment: C: Extracting MAF for a list of SNPs
18 months ago
finswimmer 11k
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209
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Comment: C: Merge contigs in fasta file
18 months ago
finswimmer 11k
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209
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Answer: A: Merge contigs in fasta file
18 months ago
finswimmer 11k
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140
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Answer: A: Which reference genome for the annotation of the 1KG variant data by snpEff?
18 months ago
finswimmer 11k
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Comment: C: checkVCF File "./checkVCF.py", line 67 errors
18 months ago
finswimmer 11k
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162
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Comment: C: Python code for extracting values from an Excel database?
18 months ago
finswimmer 11k
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150
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Comment: C: Fail to generate .bai index with samtools
18 months ago
finswimmer 11k • updated 18 months ago
RamRS 21k
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265
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Comment: C: filter unique variants from multiple VCF files
18 months ago
finswimmer 11k
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199
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Answer: A: Finding if dbSNP type in biomart
18 months ago
finswimmer 11k
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265
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Comment: C: filter unique variants from multiple VCF files
19 months ago
finswimmer 11k
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265
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Comment: C: filter unique variants from multiple VCF files
19 months ago
finswimmer 11k
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199
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Comment: C: How can I see the low frequency SNP
19 months ago
finswimmer 11k
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164
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Answer: A: How to Deduplicate files
19 months ago
finswimmer 11k
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226
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Comment: C: How to pivot pandas dataframe?
19 months ago
finswimmer 11k
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226
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Answer: C: How to pivot pandas dataframe?
19 months ago
finswimmer 11k
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179
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Comment: C: IGV - identification of sequencing errors
19 months ago
finswimmer 11k
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Comment: C: Do you know some way to remove the stop codons in an alignment and replace the s
19 months ago
finswimmer 11k
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181
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Comment: C: Aligning Multiple paired end files together
19 months ago
finswimmer 11k
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234
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Comment: C: Extracting CIGAR string from a specific region of a read in a bam file using pys
19 months ago
finswimmer 11k
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219
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Comment: C: little discrepancies gnomAD DB vs. website
19 months ago
finswimmer 11k
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229
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Answer: A: How to extract entire info column from VCF file using bcftools
19 months ago
finswimmer 11k
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273
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Comment: C: compare two columns of two files
19 months ago
finswimmer 11k
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212
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Comment: C: BBMap and Samtools show different values for mean inner distance between mate pa
19 months ago
finswimmer 11k
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212
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Comment: C: BBMap and Samtools show different values for mean inner distance between mate pa
19 months ago
finswimmer 11k
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202
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Comment: C: call haplotypes in GATK HaplotypeCaller
19 months ago
finswimmer 11k
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197
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Answer: A: Want to loop through list of BLAST objects in python
19 months ago
finswimmer 11k
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244
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Comment: C: BCF Tools Filter on 1000Genomes Annotation
19 months ago
finswimmer 11k
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272
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Comment: C: grep command on VCF
19 months ago
finswimmer 11k
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235
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Comment: C: Edit score column in bed file
19 months ago
finswimmer 11k
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282
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Comment: C: samtools fixmate: Couldn't write to output file: Broken pipe
19 months ago
finswimmer 11k
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286
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Comment: C: GATK4.1.1.0---HaplotypeCaller :HaplotypeCallerEngine - Disabling physical phasin
19 months ago
finswimmer 11k
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261
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Comment: C: How to turn current VCF into a VCF with genotype and rsID in same file
20 months ago
finswimmer 11k
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203
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Comment: C: bcftools FORMAT/FOO annotation to specific sample in multiple sample VCF
20 months ago
finswimmer 11k
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261
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Comment: C: How to turn current VCF into a VCF with genotype and rsID in same file
20 months ago
finswimmer 11k
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304
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Comment: C: shell question: How to run multiple paired end alignment in shell?
20 months ago
finswimmer 11k
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209
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Comment: C: GATK4: an error with VariantRecalibrator
20 months ago
finswimmer 11k
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242
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Comment: C: How to filter fastq paired-end reads based on Per Tile Sequence Quality
20 months ago
finswimmer 11k
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151
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Comment: C: How to retrieve cDNA sequences from EMBL for a large number of accessions?
20 months ago
finswimmer 11k
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168
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Comment: C: I have a list of chromosomes, positions, gene ids, and transcript ids (from a ge
20 months ago
finswimmer 11k
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168
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Comment: C: I have a list of chromosomes, positions, gene ids, and transcript ids (from a ge
20 months ago
finswimmer 11k
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129
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Answer: A: How to consider/get the g. positions for variants in introns?
20 months ago
finswimmer 11k
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211
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Comment: C: Bcftools Call method not detecting single nucleotide deletions?
20 months ago
finswimmer 11k
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299
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Comment: C: Approximately following the GATK recommended workflow for DNA sequence data, my
20 months ago
finswimmer 11k
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312
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Comment: C: Subsampling one bamfile multiple times?
20 months ago
finswimmer 11k
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163
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Answer: A: Should I use the same reference indexing command of bwa for WGS and WES analysis
20 months ago
finswimmer 11k
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180
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Comment: C: VCF INFO AC field for failed snps
20 months ago
finswimmer 11k
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246
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Comment: C: How to edit fasta header with underscores
20 months ago
finswimmer 11k
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173
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Answer: A: The confused result of samtools sort
20 months ago
finswimmer 11k
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246
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Answer: A: How to edit fasta header with underscores
20 months ago
finswimmer 11k
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233
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Comment: C: Install RepeatMasker "Enter path" problems
20 months ago
finswimmer 11k
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356
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Comment: C: Bam header editing
20 months ago
finswimmer 11k
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222
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Comment: C: Remove symbolic alleles for REF in a VCF file.
20 months ago
finswimmer 11k
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254
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Comment: C: Why BWA is working faster with 1 thread? Does default 4 thread option output bet
21 months ago
finswimmer 11k
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381
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Comment: C: extracting gene names
21 months ago
finswimmer 11k
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298
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Comment: C: Percent reads mapped in Picard
21 months ago
finswimmer 11k
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227
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Comment: C: Is there a paired end joiner which writes also the reads before merging?
21 months ago
finswimmer 11k
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227
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Comment: C: GC Bias in Sequence Capture - Analysis & Quantification
21 months ago
finswimmer 11k
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Tutorial: Generating consensus sequence from bam file
bam fasta consensus Tutorial
21 months ago
finswimmer 11k • updated 21 months ago
WouterDeCoster 39k
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146
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Comment: C: tabix indexing on a non vcf/bed/sam txt file
21 months ago
finswimmer 11k
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274
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Comment: C: multiple FASTA sequnces in to one full sequnce according to their chromosome num
21 months ago
finswimmer 11k
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298
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Comment: C: Percent reads mapped in Picard
21 months ago
finswimmer 11k
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298
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Comment: C: Percent reads mapped in Picard
21 months ago
finswimmer 11k
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298
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Comment: C: Percent reads mapped in Picard
21 months ago
finswimmer 11k
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268
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Comment: C: How are probabilities of insertions and deletions encoded in FASTQ?
21 months ago
finswimmer 11k
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148
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Comment: C: Datasets of genomic regions related to heart failure?
21 months ago
finswimmer 11k
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200
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Answer: A: parse of file multifasta in python
21 months ago
finswimmer 11k
1
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298
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Answer: A: Percent reads mapped in Picard
21 months ago
finswimmer 11k
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221
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Comment: C: how can I use the BQSR result for further analysis
21 months ago
finswimmer 11k
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312
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Answer: A: bcftools reheader -h
21 months ago
finswimmer 11k
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221
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Comment: C: how can I use the BQSR result for further analysis
21 months ago
finswimmer 11k
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211
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Comment: C: VCF Format in 1000 Genome
21 months ago
finswimmer 11k
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333
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Answer: A: How to extract organisms name from the headers in a multi-fasta file?
21 months ago
finswimmer 11k
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375
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Comment: C: how to extract the genomic positions and chromosome number for a list of genes
21 months ago
finswimmer 11k
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Comment: C: how to make a .tbi file of .gtf.gz?
21 months ago
finswimmer 11k
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187
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Comment: C: CollectHsMetrics base coverage output has overlapping targets
21 months ago
finswimmer 11k
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375
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Answer: A: how to extract the genomic positions and chromosome number for a list of genes
21 months ago
finswimmer 11k
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366
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Answer: A: Taking information from a .txt and converting it to fasta
21 months ago
finswimmer 11k
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275
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Comment: C: Convert BAM files to paired end FASTQ
21 months ago
finswimmer 11k
1
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248
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Comment: C: Filter Fastq file by seq
21 months ago
finswimmer 11k
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357
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Comment: C: How to check the presence of mutations of a specific gene in a specific VCF file
21 months ago
finswimmer 11k
1
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438
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Comment: C: Genomics (DNA) Pipeline - Example
21 months ago
finswimmer 11k
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248
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Answer: A: Filter Fastq file by seq
21 months ago
finswimmer 11k
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316
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Comment: C: help with python homework assignments
21 months ago
finswimmer 11k
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Comment: C: Remove duplicate readnames from a bam file
21 months ago
finswimmer 11k
1
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438
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Comment: C: Genomics (DNA) Pipeline - Example
21 months ago
finswimmer 11k
1
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236
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Comment: C: Incorrect number of AD fields (2) at 1:878906 cannot merge
21 months ago
finswimmer 11k
51
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Tutorial: Creating workflows with snakemake and conda
snakemake conda workflow Tutorial
21 months ago
finswimmer 11k
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1
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357
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Comment: C: How to check the presence of mutations of a specific gene in a specific VCF file
21 months ago
finswimmer 11k
0
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1
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357
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Answer: A: How to check the presence of mutations of a specific gene in a specific VCF file
21 months ago
finswimmer 11k
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