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5 votes
Accepted

What does a question mark ("?") mean in Picard metrics files when I expect a number (integer, float, etc.)

Picard (actually HtsJdk) uses a formatting class (via the MetricsFile class) that emits "?" for NaNs (and Infs). In your case, there seems to be a division-by-zero error during the ...
Yossi Farjoun's user avatar
1 vote

Problem while mapping reads to mtDNA (SortSam)

The first error seems to come from picard when sorting the sam file: SAMFormatException: SAM validation error: ERROR: Read name M02699:57:000000000-LG9CK:1:1119:16584:12259, CIGAR M operator maps off ...
Cloudberry's user avatar
1 vote

align to the whole hg38 genome, then split bam and collect metrics on each bam issue

This can be done, but you have to split the BAMs while keeping the full header (with the dictionary) in place for all the shards. This can be done with gatk PrintReads. One thing to remember is that ...
Yossi Farjoun's user avatar

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