Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Picard SortSam error

Answered
0

3 comments

  • Avatar
    Anthony Dias-Ciarla

    Hi Tanay Biswas,

    Thanks again for writing to the GATK forum! Let’s see if we can help you sort this out.

    So our developers informed me that your code is raising a flag that your sample is malformed. ValidateSamFile (Picard) would flag the same issue. You can use it to troubleshoot and diagnose to determine which steps you need to take to fix your bam file.

    Errors in SAM or BAM files can be diagnosed with ValidateSamFile

    I hope this helps! Please let me know what you find out and if this helps lead you to success. If you have any further questions, please do not hesitate to send them my way.

    Best,
    Anthony

    0
    Comment actions Permalink
  • Avatar
    Tanay Biswas

    Hi Anthony,

    This problem is sorted. I have again made new SAM and BAM files aligning to hg38 and used the following command:

    [tbiswas@un02 ~]$ java -jar picard.jar SortSam I=/scratch/tbiswas/TD_fixmate.bam O=/scratch/tbiswas/TD_fixmate_sorted.bam SORT_ORDER=coordinate TMP_DIR=/scratch/tbiswas/tmp/

    This time it worked. But now I'm getting error in the BQSR table generation step which I also wrote to GATK forum.

    Thanks.

     

    Regards,

    Tanay

    1
    Comment actions Permalink
  • Avatar
    Anthony Dias-Ciarla

    Hi Tanay Biswas,

    I'm happy to hear that we could solve this portion of the issue! I will continue to follow up with you on your other post.

    Thank you again for contributing to the GATK forum!

    Best,
    Anthony

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk