closedFORlunch

bedpetovcf crashes

1

I'm in a python 2.7.12 ve. I pip installed svtools. I'm trying to run: svtools bedpetovcf -i ./3717462611446476_add5.bedpe . (this is the bedpe file published as part of the LUMPY...

Error running Duphold, "expected AD field in snps VCF"

12

I'm running duphold v 0.2.1 The command I am running is: ~/install_crap/duphold/duphold -v ./results.vcf.gz -b /efs/WGS/data/WGS/ILMN_exptA/b37/KC_downsampledBAM_and_VCF/NA24385/40x/S7508/NA24385.40x.S7508.aligned.deduped.sort.bam -f /efs/WGS/data/reference/human/human_g1k_v37_modified.fasta/human_g1k_v37_modified.fasta -s ./x.vcf.gz -t 96 -o ./duphold.vcf It spins for a while, then...

FYI- all of the scripts fail to execute for me b/c this: if **name** == "**main**": main() is defined above: def main(): By moving the above if block to the...

Your install instructions state simply: """git clone https://github.com/ssadedin/ximmer.git""" """cd ximmer" """./bin/install" but this install script/binary is not part of the repo and it's unclear how to install this tool. I'm...