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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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lumpy Ouput vcf file #361

Open u1200538 opened 3 years ago

u1200538 commented 3 years ago

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} SV output

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

Thank you,

u1200538 commented 3 years ago

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)

image

Is it a right method ?