Hello,

I know Brian is sometimes around, but here is my command:

while read p; do callvariants.sh in=${p}.recal.bam ploidy=2 vcf=${p}.20score.vcf useidentity=f overwrite=true ref=ref.fsa
-Xmx50g ; done <ID java -ea -Xmx50g -Xms50g -cp /home/alessandro/software/bbmap/current/ var2.CallVariants in=ancestor.recal.bam ploidy=2 vcf=ancestor.20score.vcf useidentity=f overwrite=true ref=ref.fsa -Xmx50g Executing var2.CallVariants [in=ancestor.recal.bam, ploidy=2, vcf=ancestor.20score.vcf, useiden
tity=f, overwrite=true,
ref=Adineta_vaga.fsa, -Xmx50g]

And the console output is:

Loading reference.
Time:   0.596 seconds.
Processing input files.
Found sambamba.
Time:   230.202 seconds.
Memory: max=53687m, total=53687m, free=13311m, used=40376m
Processing variants.
Time:   12.761 seconds.

Counting nearby variants.
Time:   1.972 seconds.

Sorting variants.
Time:   1.304 seconds.
Writing VCF file.
Time:   1.064 seconds.
1838700 of 160623721 variants passed primary filters (1.1447%).

Type            Count   Rate    AD  Depth   AF  Score   Qual
Substitutions:  1669537 90.8%   158.8   341.6   0.468   43.6    23.4
Deletions:      75362   4.1%    149.5   337.3   0.446   38.4    24.2
Insertions:     93801   5.1%    151.1   340.2   0.447   40.9    24.2
Variation Rate: 1/54
Homozygous:     8887    0.5%

It gives the impression that 90% of the bases are heterozygous. Maybe I misread it, but I think this could be clarified.

It is BBmap version 39.06.

Thanks.

PS: I use biostars a lot for questions related to bbtools. Is it a correct way to use biostars? Please, admins, let me know if my questions are more annoying than helpful. Thanks a lot