
Anitha R
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Activity overview
Latest activity by Anitha R-
Anitha R commented,
The bed file consist of 399171 rows. chr1 16018 16019 . chr1 17451 17452 . chr1 56986 56987 . chr1 82733 82734 . chr1 98992 98993 .
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Anitha R commented,
While doing all this step I am getting this error after running CalculateContamination Table 1. Error: WARN KernelSegmenter - No changepoint candidates were found. The specified window sizes may...
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Anitha R commented,
Thank you, Gökalp Çelik for the clarification.
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Anitha R commented,
Hello, As I am new to the GATK pipeline, I have some questions regarding the supplement file used for the somatic variant filtering step. I call individual samples separately using Mutect2 with...
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Anitha R commented,
Thank you for the clarification. I used the hg38_af-only-gnomad.hg38.vcf file as a germline resource when calling somatic variants with Mutect2. My question is, can I use this file for both the -V ...
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Anitha R commented,
I have a doubt in somatic variant filtration step. I have completed till somatic variant calling " java -jar "$gatk" Mutect2 -R "$Ref_dir" -I "$tumor_bam_path" -I "$normal_bam_path" --tumor-sample ...