bcftools
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samtools
This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
Hi, I want to remove known variants (dbSNP and gnomad) from my VCF file. I used the command as below. bcftools isec -p test -O z -C chr9.vcf.gz dbSNP.vcf.gz gnomad.vcf.gz...
I cannot find a readme file for RoH output and recently got puzzled with results in merged.txt. I always thought "0" means non-RoH for an individual and "1" means RoH...
Hi there, Thank you for a great program! I don't exactly have an issue, but I am hoping for a sanity check on RoH so I can feel confident in...
I do have >60,000 samples to process together. I was wondering about the fastest way to process: a) Provide a bam file list to call SNPs? b) Merge into a...
When using bcftools norm to combine rows, when the genotypes are expanded the FORMAT/GT field is updated but the GL field is unchanged causing a [malformed vcf file](https://samtools.github.io/hts-specs/VCFv4.3.pdf) 1.6.2(GL) this...
Does STDEV for sure work in 1.10.2? `-e 'FORMAT/DP[*:0] > MEAN(FORMAT/DP)'` seems to work fine, but `-e 'FORMAT/DP[*:0] > STDEV(FORMAT/DP)'` filters out everything. And something like `-e 'FORMAT/DP[*:0] > (30+STDEV(FORMAT/DP))'`...
In the info field of the VCF file after bcftools mpileup and call there is a parameter called HOB "Bias in the number of HOMs number". I was wondering how...
Hi, This issue raises 2 issues related to the `SAMPLE ID` column in the output generated by `gtcheck` SETUP I have a query vcf with 3 samples, and a BCF...
Hi, Does BCFTools merge -m all also merge partially overlapping variants? When I merge two multi-sample vcf files with bcftools and then convert the complex variants in the merged vcf...
I have a vcffile with SNPs and indels where for some variants the REF and ALT (and the genotypes) are flipped with respect to the reference sequence. I tried to...
