Muhammad Shoaib Akhtar
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Recent activity by Muhammad Shoaib Akhtar Sort by recent activity-
Genevieve Brandt (she/her) thank you for clarification.
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Krithika_Subramanian can you please show the command which you ran at this stage?
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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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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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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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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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Dr N Ch Are you dealing with human genome?
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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 ...
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Genevieve Brandt (she/her) I'm sorry it didn't work. Following is error. You need permission This form can only be viewed by users in the owner's organization. Try contacting the owner of the form...
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Genevieve Brandt (she/her) I can't access form for GATK guru. It says you need permission. Please fix it.