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jiantao / Tangram

Fast Structural Variation Detection Toolbox
MIT License
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tangram_bam core dump #9

Open arawat20 opened 8 years ago

arawat20 commented 8 years ago

I am working on bam files that were generated from BWA-MEM with the output in following format:

ERR194147.232367647 65 1 9998 0 67M34S 5 18606756 0 GGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACAGAGATAACTATTGATACAACACCTTCATGACCC CCCFFFFFHHHHHJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJHHHHFFFFFEEEEEEDDDEDDDEDDDDDDDDDCDDDDDDAS:i:66 XS:i:65 RG:Z:NA12878 SA:Z:5,18606900,-,36M65S,0,0; MD:Z:0N0N0N64 NM:i:3

I am trying to run tangram_bam to generate bam files with ZA header as mentioned in the documentation. It generates following error: path/.lsbatch/1470831343.853352.shell: line 1: 2202 Segmentation fault (core dumped) command.

I am thankful for any help!!

Thanks!!

AlistairNWard commented 8 years ago

Tangram was written to work primarily with the Mosaik aligner. The code base hasn't undergone any development in a couple of years, so it is unlikely that this will be resolved. My recommendation at this point would be to use the Melt tool:

http://melt.igs.umaryland.edu/