vcflengthAdd length info field vcfkeepgenoReduce file size by removing FORMAT fields not listed on the command line from sample specifications in the output vcfcombineCombine VCF files positionally, combining samples when sites and alleles are identical. Any number of VCF files may be combined. The...
vcfsamplediffEstablish putative somatic variants using reported differences between germline and somatic samples. Tags each record where the listed sample genotypes differ with . The first sample is assumed to be germline, the second somatic. Each record is tagged with ={germline,somatic,loh} to spe...
The ideas proposed in the original pull request (#434) in July 2019 were implemented in bcftools in May 2020 (samtools/bcftools@e645749). Currently there are big files out there that follow the original proposal, see for example UK Biobank which generated VCFs with 490,541 samples using DRA...
Tags each record where the listed sample genotypes differ with . The first sample is assumed to be germline, the second somatic. Each record is tagged with ={germline,somatic,loh} to specify the type of variant given the genotype difference between the two samples. vcfflatten Removes multi-...
Multiple Nucleotide Polymorphisms: The reference and alternate sequences are of the same length and have to be greater than 1 and all nucleotides in the sequences differ from one another. bcftools filter -i 'TYPE="mnps"' eg/ex.vcf | bcftools view -H - | cut -f1-8 ## 1 25563113 . ...
vcflength Add length info field vcfkeepgeno Reduce file size by removing FORMAT fields not listed on the command line from sample specifications in the output vcfcombine Combine VCF files positionally, combining samples when sites and alleles are identical. Any number of VCF files may be combined...
usage: vcfsamplediff <tag> <sample> <sample> [ <sample> ... ] <vcf file> tags each record where the listed sample genotypes differ with <tag> The first sample is assumed to be germline, the second somatic. Each record is tagged with <tag>={germline,somatic,loh} to specify the type...
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix. - pysam/bcftools/vcfmerge.c at 6b
This is a relatively simple script. It was created for use with VCF files from RAD-style datasets. VCF file formats differ pretty dramatically so ymmv. Right now it's been tested and seems to run fine for VCF as output by both pyrad/ipyrad and tassel. ...