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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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missing pair end parameters:mean stdev #210

Closed distilledchild closed 1 year ago

distilledchild commented 1 year ago

Hi,

I was trying to run lumpy (lumpy express) with my BAM file from linked-read (10X genomics), I got the error, missing pair end parameters:mean stdev I ran samtools flagstat of the BAM file, and the result is like this.

1229732610 + 0 in total (QC-passed reads + QC-failed reads) 71294644 + 0 secondary 0 + 0 supplementary 99357616 + 0 duplicates 1196357481 + 0 mapped (97.29% : N/A) 1158437966 + 0 paired in sequencing 579218983 + 0 read1 579218983 + 0 read2 942995218 + 0 properly paired (81.40% : N/A) 1107682081 + 0 with itself and mate mapped 17380756 + 0 singletons (1.50% : N/A) 82945640 + 0 with mate mapped to a different chr 67312618 + 0 with mate mapped to a different chr (mapQ>=5)

It looks not bad, and could you give me some guidance for successful running the tool please?

brentp commented 1 year ago

Hi, this repo is for smoove. You can ask about lumpyexpress there. If you run smoove and have problems you can report the full command and the full error/output here and I can try to help.