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Variant Discovery in High-Throughput Sequencing Data

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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

GATK/Picard does not detect mates in paired-end BAM

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    Bhanu Gandham

    Hi,

     

    Take a look at this doc: https://gatk.broadinstitute.org/hc/en-us/articles/360035891231

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    jipvdinter

    Just for clarity sake, I will post the answer to my issue:

     

    After scouring the internet, I realised that BAM/SAM lines do not contain reads but alignments  (kind of a brain fart) and that paired end alignment names need to have the same query_name to be seen by processing software as being paired.

    Therefore I created a simple pysam script to remove the .1s and .2s from the reads. Tada, all lines are now recognised as properly paired reads!

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    Bhanu Gandham

    Thanks for the update jipvdinter. This will be useful to other community members! 

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