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Muhammad Shoaib Akhtar

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Latest activity by Muhammad Shoaib Akhtar
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    Muhammad Shoaib Akhtar commented,

    Genevieve Brandt (she/her) thank you for your suggestion. I already finished this task by writing a bash script. I hope using WDLs will be helpful for other people trying to do similar analysis.

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    Muhammad Shoaib Akhtar commented,

    Genevieve Brandt (she/her) Thank you so much I already tried this method but calls information didn't change. Even later, I can get only 2 haplotypes. Usually, I use bcftools consensus to make cons...

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    Muhammad Shoaib Akhtar commented,

    Genevieve Brandt (she/her) Thank you for your reply. In my dataset, several human genes are found to be duplicated using GATK's CNV pipeline. Duplicated means their copy number is 3N, 4N or 5N. Pre...

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    Muhammad Shoaib Akhtar created a post,

    Haplotypes of duplicated genes

    I run GATK Pipeline for Germline Copy Number Variation 4.1.9.0 for targeted human sequences. I found many genes with CNVs as 3N, 4N or 5N. I want to haplotype those genes to identify sequences. Is ...

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    Muhammad Shoaib Akhtar commented,

    Genevieve Brandt (she/her) thank you

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    Muhammad Shoaib Akhtar commented,

    Genevieve Brandt (she/her) Thank you for confirmation. But can you guide me if I can use any GATK tool for the purpose I'm stating below: I sequenced some genes in human samples based on Chimpanzee...

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    Muhammad Shoaib Akhtar created a post,

    De novo assembly

    Does GATK have any tool for de novo assembly?

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    Muhammad Shoaib Akhtar created a post,

    Multi-sample VCF for CNV calling

    Answered

    Hi, I'm using GATK 4.1.9.0 for Germline and Rare copy number variant discovery. I have a big dataset of more than 400 samples and I'm studying about 800 genes in each sample. I ran CNV pipeline suc...

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    Muhammad Shoaib Akhtar commented,

    Hi Genevieve Brandt (she/her), Thank you for guidance above. I got denoised copy ratio after PostprocessGCNVCaller. Here, I have 2 queries. Please guide. 1. How I may get denoised ratio of all my s...

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    Muhammad Shoaib Akhtar commented,

    Bob Handsaker Thank you.  I tried 1, 3 and 4. Unfortunately, none of those worked. I also checked my installation and reinstalled but in vain. I'm going to make wrapper scirpt. Can you please check...