lumpy Ouput vcf file

[u1200538]

Hello,

Its my first time to use lumpy. so I've just tired lumpy express with NA128768 sample as an input. As a result, I successfully got the SV vcf file, but I had discover some problem in my result. I saw the SU, PE, SR BD, SV in the header line. but at the rows, there was no "PE" contents in the INFO, FORMAT, SAMPLE column.

As you can see the below command, I correctly assigned the input file and obatined the result. I could not find any error also.

lumpyexpress -B ${bam} -S ${splt.bam} -D ${dis.bam} -K ${config} -o ${output.vcf}

Could you tell me the reason that I get this result?

Thank you,

[u1200538]

When I tried to change the bamlibs.py script, I solved these issue. (* Removed check_sq=False” from bamlibs.py, followed by @carleshf 's comment)

Is it a right method ?