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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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svtyper: error: unrecognized arguments: --max_ci_dist 0 error #238

Closed shaghayeghsoudi closed 5 months ago

shaghayeghsoudi commented 5 months ago

Hi, I ran into a a couple of new issues when trying to run smoove. I installed smoove through conda and ended up having svtyper 0.1.4. However when I run the following command smoove call -o ${OUT_DIR} --exclude ${BED} --name ${SAMPLE_ID} --fasta ${FASTA} -p 10 --genotype ${INPUT_DIR}/${SAMPLE_ID}.rmdup1.RG.bam

I keep getting the error:

svtyper: error: unrecognized arguments: --max_ci_dist 0

This is all of the flags I have when I run svtyper:

$svtyper
usage: svtyper [-h] [-i FILE] [-o FILE] -B FILE [-T FILE] [-l FILE] [-m INT]
               [-n INT] [-q] [--max_reads INT] [--split_weight FLOAT]
               [--disc_weight FLOAT] [-w FILE]
svtyper: error: argument -B/--bam is required

So it seems there is no --max_ci_dist argument.

When I exclude the svtyper from the smoove call without --genotype flag I get the output vcfs. However the weird thing is that I get no insertion in the vcf files in my samples. Can you please help me to sort out this issue to be able to proceed with my analysis? no insertion in the vcf can be due to the fact that I exclude --genotype flag? Then how can I fix the svtype error? I believe I installed the latest version from conda.

Thank you

brentp commented 5 months ago

hi, you must have the wrong version of svtyper. You'll have to get a newer version. And lumpy, which is used by smoove does not call insertions.