I am trying to run bcftools (v1.9) mpileup on 60 BAM files from WGS (~20x).
bcftools mpileup -Ou -f ref.fa $(echo $BAM_LIST) | bcftools call -vmO z -o out.vcf.gz
The job started 20 days ago. The out.vcf.gz shows that it has gone through 10 chr (~2ds/chr).
There are still 9 autosomes, 2 sex chrs, MT chr and 44 scaffolds to go through, which I estimate will take another 20 days to complete.
The log shows only the following (not updated since day of submission):
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [mpileup] 60 samples in 60 input files
out.vcf.gz is being written on daily.
I am looking for a way to make this process to go faster, say, within 2 weeks instead of 40 days.
I found a related solution here but it's for one bam at a time and I would like to call variants on all 60 samples at once.
Any help will be appreciated!