Open chadisaad opened 5 years ago
Thanks for your interest in Pisces!
OK, issue noted. As soon as I have a version available that handles that case, I'll make a note in this thread.
Hi All, on a similar note just providing more data. When I processed a bam through Hygea I see the following issue when the alignments are not primary alignments and have "*" as mentioned above -
Reads in that region -
NS500817:328:H5JL3BGX7:1:23308:7834:19270 435 1 10000 0 43H32M 8 67677964 0 MC:Z:73M MD:Z:32 PG:Z:MarkDuplicatesRG:Z:08700029 NM:i:0 AS:i:32
NS500817:328:H5JL3BGX7:1:23308:7834:19270 339 1 41527993 0 12H61M 8 67677933 0 MC:Z:25H50M MD:Z:6A54 PG:Z:MarkDuplicates RG:Z:08700029 NM:i:1 AS:i:56
NS500817:328:H5JL3BGX7:1:23308:7834:19270 163 8 67677933 60 25S50M = 67677964 104
AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTATTAGGGCTGTATATTTGGATTCAAAATATTTGGATTTTGGCCAG AA///EEEE6//EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAE6AEEEEEEAAEEEEEEEAEEEEEE/EAEEE SA:Z:GL000227.1,73741,-,42S33M,0,0; MC:Z:73M MD:Z:50 PG:Z:MarkDuplicates RG:Z:08700029 NM:i:0 AS:i:50 XS:i:20
NS500817:328:H5JL3BGX7:1:23308:7834:19270 83 8 67677964 38 73M = 67677933 -104 ATATTTGGATTTTGGCCAGGCATGGTGGCTCACGCCTGTAATCCTAGCACTTTGGGAGGCCGAGGTGGGTGGA AEEAEEAE/E/EEAEEEAEEE//<EEEEE/6EEEEEEEA//E/A/EEEA6EEEEA/EEEEAEEEEEEAA/AAA MC:Z:25S50M MD:Z:73 PG:Z:MarkDuplicates RG:Z:08700029 NM:i:0 AS:i:73 XS:i:60
NS500817:328:H5JL3BGX7:1:23308:7834:19270 435 GL000227.1 73741 0 42H33M 8 67677964 0 AATAACCCTAACCCTAACCCTAACCCTAACCCT EEEEEEEEEEEEEEEEEEEEE//6EEEE///AA SA:Z:8,67677933,+,25S50M,60,0; MC:Z:73M MD:Z:33 PG:Z:MarkDuplicates RG:Z:08700029 NM:i:0 AS:i:33 XS:i:33
NS500817:328:H5JL3BGX7:1:23308:7834:19270 163 8 67677933 60 25S50M = 67677964 104
AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTATTAGGGCTGTATATTTGGATTCAAAATATTTGGATTTTGGCCAG =C233?
NS500817:328:H5JL3BGX7:1:23308:7834:19270 83 8 67677964 38 73M = 67677933 -104 ATATTTGGATTTTGGCCAGGCATGGTGGCTCACGCCTGTAATCCTAGCACTTTGGGAGGCCGAGGTGGGTGGA ?@B@BCAD0C-CCADFF@DDF0-;DCDDF-8A=CFEBC=10A1C*BCE>8BBBC@2BBCE<BABBAB@C0BA< MC:Z:25S50M MD:Z:73 PG:Z:MarkDuplicates RG:Z:08700029 NM:i:0 AS:i:73 XS:i:60
NS500817:328:H5JL3BGX7:1:23308:7834:19270 435 GL000227.1 73741 0 42H33M 8 67677964 0 AATAACCCTAACCCTAACCCTAACCCTAACCCT BA?B@EEE?B@EEE?B?DDD>116CC<?332C= SA:Z:8,67677933,+,25S50M,60,0; MC:Z:73M MD:Z:33 PG:Z:MarkDuplicates RG:Z:08700029 NM:i:0 AS:i:33 XS:i:33 (the last alignment was not primary alignment but was still fine).
Will be wait for the version that can handle such cases.
Thanks, Satwica
thanks for the heads up!
When having multiple alignement for a same read. In SAM/BAM format, SEQ and QUAL of secondary alignments are set to ‘*’ to reduce the file size. And this cause problems for Pisces: