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bcftools isec outputs all variants instead of just the common variants

1

Hi, I have two vcf files, `ALL.autosomes.phase3.vcf.gz` and `concat_ABCD_release_2.0.1_r1_filtered.vcf.gz`. `ALL.autosomes.phase3.vcf.gz` has 2504 subjects, while `concat_ABCD_release_2.0.1_r1_filtered.vcf.gz` has 10501 subjects. After doing `bcftools isec -c none -n=2 -p isec_ABCD_ref ALL.autosomes.phase3.vcf.gz concat_ABCD_release_2.0.1_r1_filtered.vcf.gz` to...

celinehohzm

bcftools mpileup | bcftools call producing Non-zero PL Across All genotypes

1

Hi all, I have recently produced a vcf file with bcftools mpileup | bcftools call for a RAD-seq like dataset. While looking at the vcf file produced by the bcftools...

plhm

Ran into an issue with `bcftools gtcheck` (version 1.12) when comparing two VCFs, one of which has symbolic the ALT allele: ``. The output shows that the number of sites...

shankarajays

Segfault when vcf annotate uses FORMAT/GT as a column

1

When running a command like `bcftools annotate -o annotated.bcf -s sample1 -a annotation.tsv.gz -c CHROM,POS,FORMAT/GT source.vcf.gz` bcftools will segfault. To reproduce, use these inputs, where source.vcf.gz consists of ```##fileformat=VCFv4.0 ##fileDate=20210429...

cvaske

Issue in merging several vcfs

3

Hi, I installed bcftools and I ran bgzip and indexed the files using following commands. bgzip -c file1.vcf > file1.vcf.gz bcftools index file1.vcf.gz However, once I merged using following command,...

sekhwal

should bcftools norm --multiallelics - respect lexicographical order?

1

This is not an issue, but a behavior that maybe could be more optimal. I have noticed that when splitting multiallelic variants in different VCF files, you don't necessarily end...

freeseek

Empty Output File When Converting VCF to Haps

1

Hi! I am trying to convert my vcf files to hap, but I kept getting an empty output file. 1) My original vcf file looks like this, bcftools convert works...

celinehohzm

INDEL fields in the mpileup/call/norm output report raw reads

1

For the cases of INDEL, I understand that INFO=IDV/IMF fields report the number/fraction of "raw" reads, as explained in the VCF header. But I was expecting the FORMAT=DP/AD/ADF/ADR to be...

habibdanesh

bcftools view -s/-S does not recode genotypes correctly

7

By chance, I have noticed the following odd behavior. Here to reproduce the issue: ``` wget ftp://ftp.ensembl.org/pub/current_fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz gunzip Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz wget ftp://ftp.ensembl.org/pub/current_gff3/homo_sapiens/Homo_sapiens.GRCh38.103.gff3.gz (echo "##fileformat=VCFv4.2" echo "##contig=" echo "##FORMAT=" echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSM1\tSM2"...

freeseek

How to estimate Allele Frequencies from VCF file?

1

Hello all! I am trying to assess Runs of Homozygosity in BCFtools for 151 samples contained in a single VCF file. I have already run the command line: bcftools roh...

namaring