Halima Alachram
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Activity overview
Latest activity by Halima Alachram-
Halima Alachram commented,
Hi Pamela Bretscher, Thank you for your help. The pipeline is working locally. I am just having issues with some inputs which I am trying to understand. I have written to Terra Community Forum and ...
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Halima Alachram commented,
Hi Pamela Bretscher, This is exactly what I did to run the Mutect2 WDL script available here https://github.com/gatk-workflows/gatk4-mitochondria-pipeline based on the described steps from the docu...
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Halima Alachram commented,
Hi Pamela Bretscher I haven't attempted yet. I presume it could be run somehow locally since the Python scripts have well defined arguments. However, it is a cloud-based framework and some of the i...
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Halima Alachram commented,
Thank you Pamela Bretscher! One more question. Is it possible somehow to run the second part of the pipeline locally? Best regards Halima
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Halima Alachram commented,
Hi Pamela Bretscher, Thank you for the clarification! I realized that the genotypes are adjusted in a further step of the pipeline. Unfortunately, I didn't run the full pipeline since I was running...
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Halima Alachram commented,
Hi Pamela Bretscher, Here is an example of two variants where the allele fractions of alternate alleles are almost 1 and the GT is 0/1 ( heteroplasmic). chrM 152 . T C . PASS CONTQ=93;DP=4092;ECN...
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Halima Alachram commented,
Hi Pamela Bretscher, Thank you for your answer and the shared link. I have another question. In the gnomAD documention of the pipeline it is stated that " the mtDNA VCF file denotes homoplasmic gen...
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Halima Alachram commented,
Hello, As far as I understood that in the pipeline only the mapped reads are considered particularly when applying SubsetBamToChrM. Is there any reason for not considering the unmapped reads? Thanks