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6.4 years ago
Pierre Lindenbaum
161k
I'm happy to announce that some tools I've developed for Biostars have just been published in bioinformatics: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btx734/4657066
bioalcidae, samjdk, and vcffilterjdk published ! 😍 #jvarkit #java #ego https://t.co/1R7ft2RJ9P
— Pierre Lindenbaum (yokofakun@genomic.social) (@yokofakun) November 24, 2017
Those tools have been used in many of my answers on biostars.org.
- Extract specific nucleotide AND total read information (tags) from BAM
- extracting depth info from vcf
- How to extract reads with a known variant form a bam file
- Is there a limit for SAMTOOLS tview option?
- Detecting junctions from reads spanning large indels
- Choosing sam flags to extract all reads mapped to 5' -> 3' OR 3' -> 5' of reference sequence?
- Copy Sample ID from VCF file to ID column
- How to limit/filter BLAST results using NcbiblastnCommandline
- Imposing a human reference genome onto a vcf file?
- Extracting chimeric reads from mapping
- Any tool to output unmapped or mapped_with_clips reads from a BAM to two fastq files for PE data?
- Unphase a VCF file
- Switch the position of REF/ALT alleles based on AA (ancestral allele) annotations in VCF
- Which tool to calculate per site stats on vcf file?
- Calculate numbers of indels <=2 nt within sam
- Calculate reads and paired inserts covering a junction
- How to extract reads with no INDEL?
- Filetring in vcf files
- Using bcftools to change ploidy level in vcf files
- extract DP of heterozygotes from vcf file
- extracting Allele Read Counts
- Filtering a Multi-Sample VCF for variants where at least one sample meets the given conditon(s)
- Filtering multisample vcf file by
- Filtering VCF file by INFO flag
- MIN and MAX read depth for vcfutils.pl
- SnpMatrix from VCF file
- bam stats F1F2/F1R2/R1F2/R1R2/F2F1/F2R1/R2F1/R2R1
- Filter variants by specific base change pattern
- How best to parse samtools mpileup results?
- Count # of homs and hets per sample
- Genotype count in a VCF file
- Filtering no-calls from VCF file
- Selecting Variants based on annotations in a VCF file
- snp, indels and their densities in each chromosome
- Filtering on the minor allele in VCFtools
- Read alignments terminating at genomic positions.
- filtering VCF files
- Creating a consensus based on 'x' number of fasta files
- Missing alleles for a genotype in UYG VCF file
- Output per variant and per sample heterozygosity fraction from VCF.
- Extract heterozygous genotype (GT: 0/1 and 1/2) from the vcf file and calculate allelebalance.
- Can I filter based on chr_n in VCFtools
- Compare samples in one multisample VCF file
- Extracting nucleotide immediately prior to mapped read
- How to get sample names based on genotype from multi-sample vcf file
- Extract unphased genotypes from vcf file and convert to 012 matrix
- Distance to reads ends
- How to obtain anchors of specific length(eg-4 mer) from both the ends of the read.
- Taking genotypes out of a vcf file
- Generate percent of bases with quality > x from BAM file
- Count reads within region
- REF, ALT not recoded after removing individual sample in VCFtools and VCFlib
- Testing for absence of tag from info field with bcftools
- Filtering vcf file by DP
- Extracting reads with low mapping score from Bam file
- How to extract Homozygote variants froma VCF format?
- Extracting a trimmed output from a bam file
- How To Generate Variant Callings Of One Sample That Are Unique From Others In One Variant Calling File?
- How To Delete Some Rgs From One Bam File
- Filter Reads In The Sam/Bam Files By Direction Using Samtools
- Extract Regions From A Bam To A Bed File Where The Average Mapping Quality Is Below 30.
- Collect Read Pairs Where At Least One Read Is Mapped
- How To Separate Snp Variants From Indel Variants In The Same Vcf File
Love to hear that, Congratulations !
Hi Pierre. Impressive! I see that you work with R Redon? I became familiar with his work on CNVs during my PhD
Yes, Richard is my boss and the current head of our laboratory :-)
Impressive collection! Why not make it
biostarstools? ;-)Congrats!
@Pierre: Is there a way to digest these threads to get actual questions and your answers extracted in a single thread (like what I have put together here for BBMap)? Many a times your final answer may be embedded deep into comments for above threads.
@genomax I now collect all my answers in the manuals of my tools (that 's why I was able to get the post-IDs so quickly) , e.g: http://lindenb.github.io/jvarkit/VcfFilterJdk.html where most examples come from biostars.org .
Great, Congratulation Pierre! I am wondering how to pronounce "bioalcidae". Please help.
great and congratulations. Wishing you the more :)