how do i run pindel on a haploid genome

Question

[Tootiki]

i'm trying to get pindel to call for a haploid genome, but it only seems to want to give me diploid results.

my command is:

pindel \
-f REF_GENOME.fasta \
-i LIST_OF_INPUT_BAMS.txt \
-c ALL \
-o OUTPUT_FILE \
-T 20 \
--Ploidy PLOIDY_INPUT_FILE.txt

and the contents of PLOIDY_INPUT_FILE.txt are:

chr_101 1
chr_102 1
chr_201 1
chr_202 1
chr_301 1
chr_302 1
chr_303 1
chr_304 1
chr_401 1
chr_402 1
chr_403 1
chr_501 1
chr_502 1
chr_503 1
chr_601 1
chr_602 1
chr_603 1
chr_604 1
chr_701 1
chr_801 1
chr_802 1
scaffold_9 1
scaffold_10 1
scaffold_11 1

(space separated, tho i have also tried with tabs, to no avail)

it runs without error messages and produces an output file, which i then run through pindel2vcf and get a vcf file, but all the haplotypes are reported as 0/0, 0/1 or 1/1 (I.E. diploid and often even hterozygous) rather than the 0 or 1 i would hope and expect.

what should i be doing differently? thank you.

Answer 1

[Tootiki]

spoke to pindel team and got this answer:

> It looks like that we need to further work on the ploidy part and
> re-work on pindel2vcf. For now, please consider 0/0 as 0, both the
> other two as 1.