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finswimmer ♦ 11k
Role: Moderator
Status: New
Handle: @finswimmer37605
Reputation: 11100
Email: f*********@gmail.com
Joined: 11 months ago
Last seen: 3 months ago
Location: Germany

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123
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C: No reads in IGV at the positions indicated by the bed file
11 months ago
finswimmer 11k
2
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146
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A: tabix to exclude chromosomes from vcf
11 months ago
finswimmer 11k
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107
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C: snpEff for bacteria genome
11 months ago
finswimmer 11k
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C: Exclude sites on the basis of the proportion of missing data using BCFTOOLS
11 months ago
finswimmer 11k
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C: Available tools that can pick up the the alignment with highest mapping quality
11 months ago
finswimmer 11k
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177
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A: samtools SNP calling
11 months ago
finswimmer 11k
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149
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C: Any database can substitute OMIM?
11 months ago
finswimmer 11k
1
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172
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C: Replacing missing SNPs of one individual with reference alleles in a vcf file
12 months ago
finswimmer 11k
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129
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A: awk to organize bed file
12 months ago
finswimmer 11k
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150
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C: get consensus sequence from bam file with insertions
12 months ago
finswimmer 11k
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150
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C: get consensus sequence from bam file with insertions
12 months ago
finswimmer 11k
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135
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C: Extracting MAF for a list of SNPs
12 months ago
finswimmer 11k
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201
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C: Merge contigs in fasta file
12 months ago
finswimmer 11k
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201
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A: Merge contigs in fasta file
12 months ago
finswimmer 11k
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123
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A: Which reference genome for the annotation of the 1KG variant data by snpEff?
12 months ago
finswimmer 11k
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216
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C: checkVCF File "./checkVCF.py", line 67 errors
12 months ago
finswimmer 11k
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147
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C: Python code for extracting values from an Excel database?
12 months ago
finswimmer 11k
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140
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C: Fail to generate .bai index with samtools
12 months ago
finswimmer 11k • updated 12 months ago
RamRS 21k
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243
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C: filter unique variants from multiple VCF files
12 months ago
finswimmer 11k
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181
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A: Finding if dbSNP type in biomart
12 months ago
finswimmer 11k
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243
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C: filter unique variants from multiple VCF files
12 months ago
finswimmer 11k
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243
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C: filter unique variants from multiple VCF files
12 months ago
finswimmer 11k
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188
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C: How can I see the low frequency SNP
12 months ago
finswimmer 11k
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157
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A: How to Deduplicate files
12 months ago
finswimmer 11k
1
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210
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C: How to pivot pandas dataframe?
13 months ago
finswimmer 11k
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210
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C: How to pivot pandas dataframe?
13 months ago
finswimmer 11k
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165
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C: IGV - identification of sequencing errors
13 months ago
finswimmer 11k
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282
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C: Do you know some way to remove the stop codons in an alignment and replace the s
13 months ago
finswimmer 11k
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165
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C: Aligning Multiple paired end files together
13 months ago
finswimmer 11k
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221
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C: Extracting CIGAR string from a specific region of a read in a bam file using pys
13 months ago
finswimmer 11k
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205
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C: little discrepancies gnomAD DB vs. website
13 months ago
finswimmer 11k
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219
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A: How to extract entire info column from VCF file using bcftools
13 months ago
finswimmer 11k
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248
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C: compare two columns of two files
13 months ago
finswimmer 11k
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201
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C: BBMap and Samtools show different values for mean inner distance between mate pa
13 months ago
finswimmer 11k
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201
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C: BBMap and Samtools show different values for mean inner distance between mate pa
13 months ago
finswimmer 11k
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187
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C: call haplotypes in GATK HaplotypeCaller
13 months ago
finswimmer 11k
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185
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A: Want to loop through list of BLAST objects in python
13 months ago
finswimmer 11k
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230
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C: BCF Tools Filter on 1000Genomes Annotation
13 months ago
finswimmer 11k
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254
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C: grep command on VCF
13 months ago
finswimmer 11k
1
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211
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C: Edit score column in bed file
13 months ago
finswimmer 11k
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259
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C: samtools fixmate: Couldn't write to output file: Broken pipe
13 months ago
finswimmer 11k
1
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C: GATK4.1.1.0---HaplotypeCaller :HaplotypeCallerEngine - Disabling physical phasin
13 months ago
finswimmer 11k
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243
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C: How to turn current VCF into a VCF with genotype and rsID in same file
13 months ago
finswimmer 11k
1
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188
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C: bcftools FORMAT/FOO annotation to specific sample in multiple sample VCF
13 months ago
finswimmer 11k
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243
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C: How to turn current VCF into a VCF with genotype and rsID in same file
13 months ago
finswimmer 11k
1
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285
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C: shell question: How to run multiple paired end alignment in shell?
13 months ago
finswimmer 11k
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196
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C: GATK4: an error with VariantRecalibrator
13 months ago
finswimmer 11k
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230
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C: How to filter fastq paired-end reads based on Per Tile Sequence Quality
13 months ago
finswimmer 11k
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145
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C: How to retrieve cDNA sequences from EMBL for a large number of accessions?
13 months ago
finswimmer 11k
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152
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C: I have a list of chromosomes, positions, gene ids, and transcript ids (from a ge
13 months ago
finswimmer 11k
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152
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C: I have a list of chromosomes, positions, gene ids, and transcript ids (from a ge
14 months ago
finswimmer 11k
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119
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A: How to consider/get the g. positions for variants in introns?
14 months ago
finswimmer 11k
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190
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C: Bcftools Call method not detecting single nucleotide deletions?
14 months ago
finswimmer 11k
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287
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C: Approximately following the GATK recommended workflow for DNA sequence data, my
14 months ago
finswimmer 11k
1
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296
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C: Subsampling one bamfile multiple times?
14 months ago
finswimmer 11k
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144
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A: Should I use the same reference indexing command of bwa for WGS and WES analysis
14 months ago
finswimmer 11k
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170
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C: VCF INFO AC field for failed snps
14 months ago
finswimmer 11k
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231
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C: How to edit fasta header with underscores
14 months ago
finswimmer 11k
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160
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A: The confused result of samtools sort
14 months ago
finswimmer 11k
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231
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A: How to edit fasta header with underscores
14 months ago
finswimmer 11k
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221
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C: Install RepeatMasker "Enter path" problems
14 months ago
finswimmer 11k
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337
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C: Bam header editing
14 months ago
finswimmer 11k
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208
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C: Remove symbolic alleles for REF in a VCF file.
14 months ago
finswimmer 11k
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238
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C: Why BWA is working faster with 1 thread? Does default 4 thread option output bet
14 months ago
finswimmer 11k
1
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360
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C: extracting gene names
14 months ago
finswimmer 11k
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278
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C: Percent reads mapped in Picard
14 months ago
finswimmer 11k
1
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217
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C: Is there a paired end joiner which writes also the reads before merging?
14 months ago
finswimmer 11k
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211
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C: GC Bias in Sequence Capture - Analysis & Quantification
14 months ago
finswimmer 11k
11
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Generating consensus sequence from bam file
bam fasta consensus Tutorial
14 months ago
finswimmer 11k • updated 14 months ago
WouterDeCoster 39k
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137
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C: tabix indexing on a non vcf/bed/sam txt file
14 months ago
finswimmer 11k
1
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257
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C: multiple FASTA sequnces in to one full sequnce according to their chromosome num
14 months ago
finswimmer 11k
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278
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C: Percent reads mapped in Picard
14 months ago
finswimmer 11k
1
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278
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C: Percent reads mapped in Picard
14 months ago
finswimmer 11k
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278
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C: Percent reads mapped in Picard
14 months ago
finswimmer 11k
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251
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C: How are probabilities of insertions and deletions encoded in FASTQ?
15 months ago
finswimmer 11k
1
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136
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C: Datasets of genomic regions related to heart failure?
15 months ago
finswimmer 11k
1
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188
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A: parse of file multifasta in python
15 months ago
finswimmer 11k
1
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278
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A: Percent reads mapped in Picard
15 months ago
finswimmer 11k
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209
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C: how can I use the BQSR result for further analysis
15 months ago
finswimmer 11k
1
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296
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A: bcftools reheader -h
15 months ago
finswimmer 11k
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209
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C: how can I use the BQSR result for further analysis
15 months ago
finswimmer 11k
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200
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C: VCF Format in 1000 Genome
15 months ago
finswimmer 11k
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312
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A: How to extract organisms name from the headers in a multi-fasta file?
15 months ago
finswimmer 11k
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345
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C: how to extract the genomic positions and chromosome number for a list of genes
15 months ago
finswimmer 11k
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C: how to make a .tbi file of .gtf.gz?
15 months ago
finswimmer 11k
1
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1
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175
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C: CollectHsMetrics base coverage output has overlapping targets
15 months ago
finswimmer 11k
1
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345
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A: how to extract the genomic positions and chromosome number for a list of genes
15 months ago
finswimmer 11k
4
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1
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355
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A: Taking information from a .txt and converting it to fasta
15 months ago
finswimmer 11k
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258
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C: Convert BAM files to paired end FASTQ
15 months ago
finswimmer 11k
1
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234
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C: Filter Fastq file by seq
15 months ago
finswimmer 11k
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322
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C: How to check the presence of mutations of a specific gene in a specific VCF file
15 months ago
finswimmer 11k
1
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1
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408
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C: Genomics (DNA) Pipeline - Example
15 months ago
finswimmer 11k
6
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1
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234
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A: Filter Fastq file by seq
15 months ago
finswimmer 11k
0
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301
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C: help with python homework assignments
15 months ago
finswimmer 11k
3
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213
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C: Remove duplicate readnames from a bam file
15 months ago
finswimmer 11k
1
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408
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C: Genomics (DNA) Pipeline - Example
15 months ago
finswimmer 11k
1
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221
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C: Incorrect number of AD fields (2) at 1:878906 cannot merge
15 months ago
finswimmer 11k
51
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3
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Creating workflows with snakemake and conda
snakemake conda workflow Tutorial
15 months ago
finswimmer 11k
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1
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322
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C: How to check the presence of mutations of a specific gene in a specific VCF file
15 months ago
finswimmer 11k
0
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322
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A: How to check the presence of mutations of a specific gene in a specific VCF file
15 months ago
finswimmer 11k
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