fix: invalid bam flag using picardtools #1027
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khurrammaqbool
requested review from
hassanfa,
ashwini06 and
ivadym
as code owners
Codecov ReportBase: 99.25% // Head: 99.25% // Increases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## develop #1027 +/- ##
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Coverage 99.25% 99.25%
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Files 28 28
Lines 1746 1747 +1
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+ Hits 1733 1734 +1
Misses 13 13
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ivadym
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Nov 27, 2022
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This was referenced Nov 28, 2022
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This PR:
The bam files generated multiple errors showing an invalid bam flag for numerous reads. Samtools could fix a few of them, but not all. Picard tools fixmateinformation command performs better than samtools and fixes the invalid bam flags.
The possible origin of these errors could be concatenated fastq file. The current PR fixes the issue, but it would be better to use each fastq as input and merge bam files instead.
Fixed: invalid bam flag using
Picard tools.Review and tests: