bcftools

bcftools copied to clipboard

Symbolic alleles not supported when using consensus _2

2

Hello! Im using bcftools 1.15.1 : `bcftool consensus -H 1 -f ref.fa hifi_on_primary_phased.vcf.gz > hap1.fasta` error: ``` Symbolic alleles other than , or are currently not supported, e.g. "" at...

sashulkaSh

[E::bcf_translate] Unchecked error (2) at chr10:10331, exiting

2

Hi，when I concatenate some vcf file，it report this error. I don't understand the `at chr10:10331` . What does that mean?

hanguojun007

consensus --iupac-codes outputting ambiguity on GT=1/1 sites

6

Hi all, This is similar to an issue posted before to which I didn't find a solution. I am using bcftools consensus with --iupac-codes and the output has ambiguity codes...

ribeirots

Heterozygous SNP sites calling

3

Hello, I am currently using the mpileup | bcftools call pipeline to call multiple SNPs in diploid organisms. If I understood this correctly, the call command exploits the genotype likelihoods...

ettorefedele

Annotate fail to add INFO when match structural variation by POS,~ID,REF,ALT

3

Hi, I am using bcftools 1.15.1. I want to add INFO for a vcf file of structural variations. The vcf is like: ``` chr1 10627 ID1 N . PASS some_INFO...

Han-Cao

I am trying to use the +fixref plugin to fix a VCF after a liftOver operation. I have two issues. The first issue relates to the following code: ``` else...

freeseek

Different outputs from **bcftools norm** command using different version of bcftools

1

Dear developers, I have a problem regarding the different outputs from **bcftools norm** command using different version of bcftools. If I use the bcftools version 1.7-2, the ALT column of...

RENXI-NUS

bcftools consensus error: No such sample

1

Hi, I'm running consensus with the following code: `bcftools consensus -f int.fa -H 1 -s H1 haplotype.vcf.gz > id1.fa` The input haplotype.vcf is like > ##fileformat=VCFv4.2 #CHROM POS ID REF...

WeiCSong

VCF parse error:FILTER ' PASS' is not defined in the header

1

Dear all, I 'm compressing vcf with the following code: bcftools view white_yakXcow.FI.vcf -Oz -o white_yakXcow.FI.vcf.gz The input white_yakXcow.FI.vcf is like ##fileformat=VCFv4.2 ##FILTER= ##ALT= ##FILTER= ##FILTER= ##FILTER=   ...

wzp99

bcftools annotate using large annotation VCF is slow regardless of input VCF size

11

Hi, I'm trying to annotate a VCF with only 248 variants using the gnomad genomes VCF as annotation and it takes about 2 hours to run. Both the input VCF...

oleraj