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                                            DavidStreid

Error "exit status 83" for lumpy-filter

I am experiencing the same issue w/ smoove v2.7 - does this mean I am using the correct version? I have included the error below (editing filenames). Would you be...

bamutil diff - Get record for every read being compared

Sorry for the delay - my issue was that I'm noticing that most reads weren't in the diff output and I was wondering why. That it only captures diffs, addresses...

MergeVcfs and SortVcf lose NULL sample values when SAMPLEs in headers need to be reordered

Please let me know if I should move this issue into [Picard](https://github.com/broadinstitute/picard/issues)

MergeVcfs and SortVcf lose NULL sample values when SAMPLEs in headers need to be reordered

I'm also observing this with SortVcf ``` $ gatk SortVcf -I chr1.input.vcf -O chr1.input.sorted.vcf 2> /dev/null Tool returned: 0 $ grep -E "CHROM|101" chr1*vcf chr1.input.sorted.vcf:#CHROM POS ID REF ALT QUAL...