version 1.12 call only outputs GT

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
25/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
c
Domain
bioinformatics, cli

Research direction

Re-run the exact bcftools mpileup and bcftools call pipeline with v1.9 and v1.12, using the referenced FASTA, BAM, VCF, and TSV inputs. Compare the FORMAT fields in both outputs and inspect the call and mpileup command documentation or entry points; done means the v1.12 behavior is explained and the supported way to retain PL and DP is identified.

Written by the indexing model from the issue text.

Description

requires-test-case

Hi, I'm running the same command with bcftools v1.9 and v1.12:

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 -Aim -C alleles -T ALL.chr22.sites.tsv.gz -Oz -o test.vcf.gz

I found that using v1.9, there are three fields: GT, PL and DP, but using v1.12 there is only the GT field.
I'm wondering whether this is the default behavior of v1.12, if yes , how can I get the other fields?

Thanks!

Dominant language
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