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.