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
I used the following command on the vcf file to calculate roh. My question is how can I have this plot? bcftools roh -G30 --AF-dflt 0.4 file.vcf plot source :...
I have seen some differences in recall and precision with the big changes in the mpileup command in v1.13 with Nanopore data. The first thing to say though is v1.13...
Hi, could someone explain me why the feature type for a line in a GFF is not taken from the third GFF filed but `bcftools csq` expect each gene and...
hello， In my vcf after splitting multiallelic sites, the info was separated wrongly, like this Before splitting ``` chrM 16189 . T C,A . PASS AS_FilterStatus=SITE|weak_evidence,base_qual,strand_bias,possible_numt; GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:3,2016,22:0.995,4.028e-03:2041:1,814,6:2,1101,3:0,3,659,1379 ``` After...
I would like to present a test report for this plugin because I found that someone else met the same issue before, but with few clear answer. The purpose of...
I tried imputing gender of samples with guessploidy. In fact I have the gender status of some samples and others I don't have. I used guessploidy on the vcf file...
Hi there, I was having the same problem in #933 and the fix below isn't working from the files from NCBI here: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/ > Both specifying the column orientation and...
Hello! In my vcf after splitting multiallelic sites, it has two or more variants on one site. like this: ``` 10 89623861 . T A 10 89623861 . T C...
Hi, While attempting to check allele Frequency with 1000g using the +af-dist plugin, i got this output [msr52@login-e-10 v1_chip_extra]$ head data.dist.txt PROB_DIST 0.000000 0.100000 0 PROB_DIST 0.100000 0.200000 0 PROB_DIST...
as like title, if one line like this "**chr1 11140624 . C A,\* 366.64 . AC=1,1;AF=0.250,0.250;AN=4;BaseQRankSum=-8...**" , in "A,*", symbol star indicate there is one sample lose REF C, So...
