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Same pipeline for exome seq variant calling with different results

Hello Gatk team,

we have been running a pipeline using fastp, bwa-mem, and gatk with hard filtering to perform snp calling on exome seq data. Although the coverage statistics for fastq files is similar, we obtain a huge difference in the number of reads per snp. We wonder if it could be caused by hard filtering. Otherwise, could you suggest any idea of what can be going on?

Thanks in advanced.


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @paumarc

    I will need some more information to help you with this. Would you please post the exact commands you are using in your pipeline, the version of gatk you are using and the some records of the differences you see in the number of reads per snp.
    Thank you.


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