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The warning message says mate not found. But samtools flagstat show 100% paired.
24582834 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
2126 + 0 supplementary
0 + 0 duplicates
24582834 + 0 mapped (100.00% : N/A)
24580708 + 0 paired in sequencing
12292464 + 0 read1
12288244 + 0 read2
24580708 + 0 properly paired (100.00% : N/A)
24580708 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
*****WARNING: Query A00611:74:HVLJGDRXX:2:2277:20482:12759 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.
*****WARNING: Query A00611:74:HVLJGDRXX:2:2277:20871:27461 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.
*****WARNING: Query A00611:74:HVLJGDRXX:2:2277:20961:24925 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.
*****WARNING: Query A00611:74:HVLJGDRXX:2:2277:21151:34585 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.
*****WARNING: Query A00611:74:HVLJGDRXX:2:2277:21160:4225 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.
*****WARNING: Query A00611:74:HVLJGDRXX:2:2277:21368:23813 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.
The underlying reason is that we first filtered out -q 30 and -F 1804.
So those paired reads from bwa-mem will still have a flag 99 or something similar, even their mate is removed due to low q score.
Don't think this is a bug, but might need to have a note here and think about which way makes more sense
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The warning message says mate not found. But
samtools flagstatshow 100% paired.The underlying reason is that we first filtered out
-q 30and-F 1804.So those paired reads from bwa-mem will still have a flag 99 or something similar, even their mate is removed due to low q score.
Don't think this is a bug, but might need to have a note here and think about which way makes more sense
One example here:
after filtering, the first read is retained and the flag is still 99.
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