SAM: why NM and MD tag are changed by the picard tool SetNmMdandUqtag ?

Question

[quentin54520]

Hello all,

For my human WGS i use BWA mem and MarkduplicateSpark. Then i used SetNmMdAndUqtag ad i would like to know if it's normal that the tag NM and MD (already present before using this last tool) are change by this tool and if yes, why? For exemple this the same read before and after using SetNmMdAndUqtag, you can see that the NM tag is NM:i:0 before and NM:i:1 after, and the tag MD is MD:Z:85 before and MD:Z:0N84 after.

Thanks in advance for your help :-)

samtools view G632_DA_C001KUN_HY322DSXX.DUAL310.trimmed.align.sort.merged.filtered.dedup.bam | grep 'V1:1:HY322DSXX:3:2512:16188:6010'
V1:1:HY322DSXX:3:2512:16188:6010 81 chr1 10000 0 66S85M chr8 58017675 0 TGATATTTCATGTGAATGAGTAGCTGAAAGGTGCTAATGAGGTATTTAATACTGGTACTAGAATCAATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC FFFFFFFFFFFFFFFFFF:FFFF:F:F:FFFFF:FFFFFFFFF:FFFF:FFFFFFFF:FFF,FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFF,FFFFFFFFFF,FFFFFFFFFF SA:Z:chr8,58017769,-,67M84S,0,0; MC:Z:151M MD:Z:85 RG:Z:G632_DA_C001KUN_3_HY322DSXX.DUAL310 NM:i:0 AS:i:85 XS:i:84



samtools view G632_DA_C001KUN_HY322DSXX.DUAL310.trimmed.align.sort.merged.filtered.dedup.fixed.bam | grep 'V1:1:HY322DSXX:3:2512:16188:6010'
V1:1:HY322DSXX:3:2512:16188:6010 81 chr1 10000 0 66S85M chr8 58017675 0 TGATATTTCATGTGAATGAGTAGCTGAAAGGTGCTAATGAGGTATTTAATACTGGTACTAGAATCAATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC FFFFFFFFFFFFFFFFFF:FFFF:F:F:FFFFF:FFFFFFFFF:FFFF:FFFFFFFF:FFF,FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFF,FFFFFFFFFF,FFFFFFFFFF SA:Z:chr8,58017769,-,67M84S,0,0; MC:Z:151M MD:Z:0N84 RG:Z:G632_DA_C001KUN_3_HY322DSXX.DUAL310 NM:i:1 UQ:i:37 AS:i:85 XS:i:84