Muhammad Shoaib Akhtar
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Activity overview
Latest activity by Muhammad Shoaib Akhtar-
Muhammad Shoaib Akhtar commented,
Genevieve Brandt (she/her) thank you for clarification.
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Muhammad Shoaib Akhtar created a post,
GATK Germline CNV Discovery
This is just an exploratory question for my understanding. How GATK's germline CNV calling works in single sample mode vs cohort mode?
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Muhammad Shoaib Akhtar commented,
Krithika_Subramanian can you please show the command which you ran at this stage?
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Muhammad Shoaib Akhtar commented,
Dr N Ch I think you can use same as I uploaded in above comments. For all autosomal chromosomes, it should be as follows: Please add chromosome names as they're in your reference genome e.g., it m...
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Muhammad Shoaib Akhtar created a post,
GATK tutorial workflows
AnsweredI have a basic question to GATK team: In GATK's best practices workflow guides, some workflows are shown. Are they copyright free? Can I reuse them to illustrate pipelines I used in my research? Fo...
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Muhammad Shoaib Akhtar commented,
Mehdi Sorry for delayed response. Your strategy seems fine to me. To rename chromosomes, I think you can simply use 'sed' command in linux shell. Use to 'man sed' to see 'sed' options.
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Muhammad Shoaib Akhtar commented,
Mehdi make contig ploidy priors as per your reference. You can make this table in accordance with your reference. Yes, all of the contigs in the SAM/BAM files (in fact in the read count files) shou...
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Muhammad Shoaib Akhtar commented,
Dr N Ch genome on which you're working is diploid? If so then just replace contig_names with your contigs except for chrX and chrY.
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Muhammad Shoaib Akhtar commented,
Dr N Ch Are you dealing with human genome?
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Muhammad Shoaib Akhtar commented,
Dr N Ch Here's the one I used. You can customize as per your needs. CONTIG_NAME PLOIDY_PRIOR_0 PLOIDY_PRIOR_1 PLOIDY_PRIOR_2 PLOIDY_PRIOR_3chr1 0.01 0.01 0.97 0.01chr2 0.01 0.01 0.97 0.01chr3 0.01 ...