Hello, I have a 30X simulated bam file from running another pipeline and I was trying to run depth-of-coverage tool to get DOC but kept running into problems:
1. When I first ran depthofcoverage, it gave me an error that says my file has no readgroups, so I tried to use Picard AddOrReplaceReadGroups
2. But then after running the tool, depth-of-coverage gave me an error that said my new bam file has incorrect order of chromosomes, the exact error was
Lexicographically sorted human genome sequence detected in reads.
3. So I tried to run samtools sort on this bam, but it tells me the "EOF marker is absent and that my bam file was probably truncated". I went back to check my bam file and it looks like the size of my bam went from 100GB to 3GB after running Picard AddOrReplaceReadGroups.
So I am really confused what is happening here. I should note that when I ran Picard AddOrReplaceReadGroups, it gave me an error message that says SAM validation error: "WARNING: Read name FC:0:0:368:54711, No M or N operator between pair of D operators in CIGAR" . After I set the validation stringency to silent, it ran through.
Thank you so much!
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