Joint variant calling

Question

[arash.iranzadeh1980]

Hi,

I have 1500 bacterial clean and sorted alignment bam file and I want to call variant and produce a multisample vcf file including 1500 samples. I am going to use GATK and bcftools and then compare results. Bacteria are haploid. In the following commands, -ploidy must be set to 1 or 1500?

bcftools call -m -v --ploidy 1 -O z -o variant.vcf.gz mpileup.bcf

java -jar $GATK -T UnifiedGenotyper -R reference.fa -I bam.list -glm BOTH -stand_call_conf 30 -ploidy 1 -o call.vcf

[Medhat]

why you are not using HaplotypeCaller?

The HaplotypeCaller is a more recent and sophisticated tool than the UnifiedGenotyper. Its ability to call SNPs is equivalent to that of the UnifiedGenotyper, its ability to call indels is far superior, and it is now capable of calling non-diploid samples. As of GATK version

3.3, we recommend using HaplotypeCaller in all cases, with no exceptions.

--sample_ploidy / -ploidy

Ploidy per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy). Sample ploidy - equivalent to number of chromosome copies per pool. For pooled experiments this should be set to the number of samples in pool multiplied by individual sample ploidy.

[mgdias.jose]

If you use the HaplotypeCaller, you should use --ploidy 1. I assume that for bcftools the logic should be similar