dumpSTR index error running HipSTR VCF output

[limrock1]

Hi,

I ran HipSTR (v0.6.2) on a single TR region (HD on chr4) as follows

HipSTR --bams SAMP1.cram --fasta genome.fa --silent --regions HipSTR.HTT.bed --lib-from-samp
--def-stutter-model --max-str-len 1200 --min-reads 15 --output-filters --str-vcf SAMP1.vcf.gz ;

I then ran dumpSTR (v4.0.0) with the following command:

dumpSTR --vcf SAMP1.vcf.gz --vcftype hipstr --hipstr-max-call-DP 1000 --hipstr-min-supp-reads 1
--verbose --out SAMP1_L1_filter

and got the following error:

Overwriting the preexisting info AC field
Overwriting the preexisting info REFAC field
Traceback (most recent call last):
File "/software/miniconda3/bin/dumpSTR", line 8, in
sys.exit(run())
File "/software/miniconda3/lib/python3.8/site-packages/trtools/dumpSTR/dumpSTR.py", line 1245, in run
retcode = main(args)
File "/software/miniconda3/lib/python3.8/site-packages/trtools/dumpSTR/dumpSTR.py", line 1183, in main
record = ApplyCallFilters(record, call_filters, sample_info, invcf.samples)
File "/software/miniconda3/lib/python3.8/site-packages/trtools/dumpSTR/dumpSTR.py", line 569, in ApplyCallFilters
filt_output = filt(record)
File "/software/miniconda3/lib/python3.8/site-packages/trtools/dumpSTR/filters.py", line 505, in call
if "/" in record.format["GB"][samples_to_check][0]: delim = "/"
IndexError: index 0 is out of bounds for axis 0 with size 0

Any ideas what might be going on here?
Thanks,
Sean.

[LiterallyUniqueLogin]

Yeah, I think I know the bug - I believe it's the same as what a teammember sent me recently. Let me try to get the change I'm intending out today and see if that fixes it for you.

[limrock1]

K, thanks.

[LiterallyUniqueLogin]

TRTools 4.0.1 is out on PyPI and is in the process of being released on bioconda, I'll ping when that's done. Please upgrade and let me know if that fixes the issue.

[LiterallyUniqueLogin]

It is now published on bioconda as well. I'm closing this issue, feel free to post back if there are still problems.