Picard MergeBamAlignment's CLIP_OVERLAPPING_READS not working?

I have created a toy unmapped bam called u.bam with two pairs of overlapping reads:
181221_A00719_0016_BH5FY3DRXX:1:1101:10004:11584 77 * 0 0 * * 0 0 TGAAAACAAGCACAGCTTCATAGCATAGAATGGGATTGGGGGTCCAGTCTTCCCAGAATATTTTCTTTCCCATCTTCCCCTTGGGGAACAGATTCACCCAC :FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:18122.1
181221_A00719_0016_BH5FY3DRXX:1:1101:10004:11584 141 * 0 0 * * 0 0 TAACTAACTTGTTCAAGGTCTCCCAGCTAGGATCTAGCAGAAAGATCAGGAAGGTATCACAAGGAAGGTGGGTGAATCTGTTCCCCAAGGGGAAGATGGGA FFFFFFFF,F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFF:FFFFFFFF:FFFFFFFFFFFF RG:Z:18122.1
181221_A00719_0016_BH5FY3DRXX:1:1101:10004:19257 77 * 0 0 * * 0 0 AATTATACTACGGTGGAGATGATTCATTTAGAAATGAGACTGAACAGGTCTGGGGGGCATAAGTACGTTTTGCAAGCATGTGGCATGGCCCAGATTCCTAT FFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:18122.1
181221_A00719_0016_BH5FY3DRXX:1:1101:10004:19257 141 * 0 0 * * 0 0 CGATATTCAGAAGGACTCCCACCAAGAAGCCACAGGTGCAAGTTGAGAGAGAATCATCAGTAGGAGAGTATAGCTGCTATAGGAATCTGGGCCATGCCACA FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:18122.1

But when I feed them through this command. Nothing is soft clipped in the output o.bam as described in the doc. Why is that?
java -jar /usr/bin/picard/picard-2.17.10.jar SamToFastq I=u.bam F=/dev/stdout INTERLEAVE=true|/usr/bin/bwa/bwa-0.7.17/bwa mem -M -p /home/db/hg38/hs38DH.fa /dev/stdin | java -jar /usr/bin/picard/picard-2.17.10.jar MergeBamAlignment UNMAPPED=u.bam ALIGNED=/dev/stdin O=o.bam R=/home/db/hg38/hs38DH.fa CLIP_OVERLAPPING_READS=true ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true

Answers

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    Hi @ymc you might be seeing these errors due to invalid SAM record formats. There is an extensive discussion of this problem on the forum.

    It might be helpful to generate a test set from a true sam file with good alignments by just changing up the headers to make them look overlapping.

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