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
Dear pd, Thank you for the software. When I use bcftools "consnensus genome" to get a pesudogenome with 20 chromosome numbers (genome size: about 2.5G), I only got three chromosomes...
Hi, I used this command to call variants with bcftools, but I felt that bcftools ran not fast as before, it has run over 18 hours, only called 11Mb sequence...
Is it possible to use fields as the target of a match? For example, I'd like to do something like the following: `bcftools view --include 'FORMAT/SP ~ ALT'` Thanks!
Hi, My data consists of about 4000 subjects with a vcf file for each and the aim is to merge them all together and split by chromosomes. I used "bcftools...
I am genotyping 10 individuals with _mpileup_ and _call_ commands and I am getting some strange results. I am using this code: bcftools mpileup --skip-indels --annotate FORMAT/AD,FORMAT/DP,INFO/AD -C 0 -d...
What's the expected behavior when applying `norm -m-` to split multiple alleles when there is a * ALT? After filtering against gnomad to get rare variants I'm left with a...
I have a VCF file with the following FORMAT fields: AU, TU, GU, and CU. I want to calculate the Allele Frequency (AF) for each variant based on the ALT...
I have been using bcftools stats, but I'am confused about the "Genotype concordance by non-reference allele frequency (SNPs) dosage r-squared". When I set --af-bins "0.01, 0.02, 0.03, 0.04, 0.05, 0.06,...
Hello, When merging VCFs, I would like to not allow multiallelic records and only merge by ID, does combining multiple --merge options works ? bcftools merge -m none -m id...
Similar to samtools/samtools#1909, this is a companion pull request to samtools/htslib#1665. Now that `hts_open("-", "w")` / `hts_close()` no longer actually closes stdout. Close it explicitly at the end of `main()`...
