We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Cigar after picard MergeBamAlignment
I got confused by the CIGAR in bam file. after MergeBamAlignment.
I have reads in uBam. Then it's converted into fastq and trimmed on 5' side. Then aligned with STAR and MergeBamAlignment the mapped Bam with the uBam to recover the tags.
Below is an example:
original fastq read
I did 5bp triming on the 5'side.
After STAR mapping.
K00206:101:HH7C2BBXX:1:1101:10003:10141 16 19 9113177 255 32M975N89M * 0 0 TGCCAACTGAGCAGCCTCCTCTACGGTCTTTCCTTGCTCTACATGGAAGAGGGCAAGTCTGGCCAGATTCACCTTCAGGATACTTTCCCCATGTCCTGTGGTTGAAACGGCTCCAAGGTTA JJJJJJJJJFJFAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ NH:i:1 HI:i:1 AS:i:120 nM:i:0 NM:i:0 MD:Z:121 jM:B:c,22 jI:B:i,9113209,9114183 XS:A:-
K00206:101:HH7C2BBXX:1:1101:10003:10141 16 19 9113177 255 5S32M975N89M * 0 0 TGCCAACTGAGCAGCCTCCTCTACGGTCTTTCCTTGCTCTACATGGAAGAGGGCAAGTCTGGCCAGATTCACCTTCAGGATACTTTCCCCATGTCCTGTGGTTGAAACGGCTCCAAGGTTATTATC JJJJJJJJJFJFAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA MD:Z:0T0G0C0C1A1T1A0G0C0A0G0C2C1T0C1A0C0G0G0T3T1C0T1G1T0C0T0A0C1T0G1A0A0G1G1G1A0A1T1T1G0C0C0A0G0A0T1C0A0C0C0T0T0C1G0G0A1A1T0T0T0C0C0C1A3C0C1G0T0G0G0T0T1A0A0A1G0G0C0T0C0C0A1G0G0T1A0 PG:Z:STAR RG:Z:E11_m_Mut-6-2_A2B5 NH:i:1 NM:i:87 UQ:i:3524 AS:i:120
It's aligned to the reverse strand. The SEQ in bam is fine. But the CIGAR has "5S" on the left. Is it supposed to be on the right? When I visualise the bam after MergeBamAlignment, it's full of mismatches because of the CIGAR.