Qualities of bases accepted for local realignment

stokerstoker BergenMember

Dear GATK team,
I try to adjust Solid data to run in GATK. Unfortunately the problem is qualities of bases. I tried to adjust all of them to Illumina format (+33) but it seems they are not accepted during the following step:
2. Perform realignment of the target intervals

How can I adjust my qualities (or optionally whole Solid data) to work fine with GATK?

Answers

  • stokerstoker BergenMember

    Here is part of my alignment file. I have used tools to "repair badly formatted bam" but it didn't help.
    Data originate from solid platform.

    @/6;@6///=22?///@/==>;@:-.669/.226=3 XM:i:0
    1_142_102 16 chr13 46065678 255 48M * 0 GTTTCTACTTGTTTTGGTTTAATGTTAAATCTTCCTCTTGAGTTATGT U___^[__________________^^__________[[_________ XA:i:0 MD:Z:48 NM:i:0 CM:i:0
    1_142_1792 0 chr22 37881913 255 48M * 0 CCTTAGGCCAGGGGCCACCCCCAGGGCCCAATGTCACCCACTTGTCAC ^[____]]^^[[_________[[______^^^]]^]]]]]] XA:i:0 MD:Z:48 NM:i:0 CM:i:0
    1_142_1257 16 chr5 55264209 255 48M * 0 GGTTTTTCTGGAGGCACTAAAAGGGATTAATTAGCATCTTTCAGAAAG WW___ZZ^^_____________QQ___]]NN_____NN XA:i:0 MD:Z:48 NM:i:0 CM:i:0
    1_138_1702 4 * 0 0 * * 0 0 GGGCAGTCGGTGCTGGACGCACGGGCAATTCAATTCCATCGGGAGTACT 6;=22>;;368?-/[email protected]->@2-28>;3-62. XM:i:0
    1_143_48 16 chr5 149006686 255 48M * 0 GTATGGCCCTGGGAAGCTGTACCAGGTGACAAGCAACATCAGTGGGAC ____]]__________________________________________ XA:i:0 MD:Z:48 NM:i:0 CM:i:0
    1_142_1998 0 chr17 26575285 255 48M * 0 GCACAGGCTCAATAAAGCAAGTCAAAGCACAGCTTATCTCTGTGTCTC ____________^^_______\___QQ___QQ_\Z\^___^]
    [Y XA:i:0 MD:Z:48 NM:i:0 CM:i:0
    1_143_1530 16 chr3 49866925 255 48M * 0 TCGAAGCCTGTCCTTACCTAGGGTGGAAGGAAGAGATGAGTGGGCCAG 1!2WVMDU__/!%GQ^PQ____^^]]_________^^]][[]]_ XA:i:0 MD:Z:48 NM:i:0 CM:i:4
    1_143_1308 16 chr13 111536163 255 48M * 0 TTCAGATTCCTTTGTCTGTAACAAGATAAGTGTTCAGACACACAGTTT ]_____ZZ^^ZZ^^__________________NM^_______ XA:i:0 MD:Z:48 NM:i:0 CM:i:0
    1_143_1109 0 chr10 125269784 255 48M * 0 TTTTCCCTATCTCCTGACTCAGGCAACCTCATCATTTTCCTCTGAAAG __]]__ZPU[XTW_WU\^_QPPQ_WWNN_QQ//_QQNN_N=!!URT XA:i:0 MD:Z:48 NM:i:0 CM:i:2

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @stoker,

    You shouldn't need to do any adjusting on your SOLiD data files; the GATK is able to interpret the SOLiD format natively. Did you try running on your original files? If you did and it failed, what was the error message?

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