bcftools
bcftools copied to clipboard
samtools
This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
Hello, I am trying to join duplicate positions that are created when I break down MNPs to SNPs. I seem to get two records one classed as an MNP and...
Hi this is currently the last case of confusion: In this example the protein lengths are 260 and 1020 amino acids for the two different transcripts. This mutation now effects...
Dear @pd3 I am using bcftools roh (version 1.12; `bcftools roh -G30 -e - -O r vcf.gz`) to detect regions of autozygosity in whole genome sequencing data. The vcf.gz contains...
This is a bit of a weird corner case, but if I have a VCF file with two identical variants `chr1 20000 A G`: ``` (echo "##fileformat=VCFv4.2" echo "##contig=" echo...
I've a vcf entry like: ``` chr 8083 . GG GAA,GA 40008.9 . AB=0.137227,0.819141;ABP=1627.35,1260.12;AC=1,1;AF=0.5,0.5;AN=2;AO=195,1164;CIGAR=1M1I1X,1M1X;DP=1421;DPB=1521.5;DPRA=0,0;EPP=4.89224,29.8739;EPPR=5.49198;GTI=0;LEN=3,1;MEANALT=4,4;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=188.157;PAIRED=1,0.993127;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=7396,44298;QR=537;RO=14;RPL=113,704;RPP=13.7118,114.076;RPPR=3.63072;RPR=82,460;RUN=1,1;SAF=94,596;SAP=3.55595,4.47287;SAR=101,568;SRF=9;SRP=5.49198;SRR=5;TYPE=complex,snp ``` Unfortunately, `bcftools consensus` chooses the first of allele, hence the less frequent one, in this...
I am working on annotating a vcf file using a bcf dbSNP. But it seems that records with N as an ALT field don't get annotated. But surprisingly to me,...
I hope this is not me misusing bcftools, but there seens to be an issue between bcftools norm v1.9 and v1.12 (I did not check intermediate versions). ``` chr1 13324...
Using the latest release version of bcftools-1.12 I've been hitting an issue where it seems to lose entries when widening a query range /data/bcftools-1.12/bcftools view /mnt/results/pipeline/sample/sample.g.vcf.gz -r chr17:150000-170000 -O v...
Consider the following [BAM-file](https://github.com/samtools/bcftools/files/6305196/deletion_issue.bam.gz) with [reference](https://github.com/samtools/bcftools/files/6305202/NC_045512.2.fasta.txt) and generate a consensus sequence using the following commands with bcftools version 1.12: ``` bcftools mpileup \ --max-depth 1000000 \ --max-idepth 100000 \ --annotate...
Hi, I'm running the same command with bcftools v1.9 and v1.12: ```sh bcftools mpileup Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz -I -E -a 'FORMAT/DP' -r 22 --max-depth 1000 -T ALL.chr22.sites.vcf.gz smp_possorted_nodup.bam -Ou | bcftools call...
