Vempalli Fazulur
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Activity overview
Latest activity by Vempalli Fazulur-
Vempalli Fazulur commented,
Dear Gokalp Celik, Thank you so much for confirming. Thanks & Regards Fazulur Rehaman
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Vempalli Fazulur commented,
Dear GATK team, Thank you so much for your quick response. I have data for 15 healthy control samples from which i can create panel of normals. However these healthy controls are not from same tis...
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Vempalli Fazulur created a post,
GATK Somatic CNV Tumor only calling
Dear GATK team. I am trying to perform somatic CNV calling on a custom panel of approximately 1,200 genes in tumor-only mode. I found the following workflows for somatic CNV calling (recently updat...
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Vempalli Fazulur commented,
Dear Genevieve, Thanks a lot for WDL link. I will try that. I have used sentieon dnaseq pipeline to generate vcf on my data which internally use bwa for alignment & GATK for variant calling. Thanks...
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Vempalli Fazulur created a post,
GATK Haplotypecaller - different variant calls from bam generated using converted fastq
AnsweredDear GATK team, This is general question regarding different results in variant call results from converted fastq Vs original fastq. I converted back bamtofastq using the below link and perform ali...
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Vempalli Fazulur commented,
Dear Genevieve, Thanks for your quick response. Yes, I agree that there are not enough reads to support variant allele in our WGS sample. Thanks & Regards Fazulur Rehaman
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Vempalli Fazulur commented,
Dear Genevieve, Sorry for late response and thanks for your suggestion on running WGS without intervals. I tried this way and got more variants but not the above ones which I got with whole exome. ...
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Vempalli Fazulur commented,
Dear Genevieve, Please find below the igv screenshots of both positions from input bam files. 1. 12:109639296 2. 15:51201293 Thanks In Advance Fazulur Rehaman
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Vempalli Fazulur commented,
Dear Genevieve, Sorry for uploading the testdata and thanks for looking into this. As per your suggestion, I generated igvscreenshots of bamout files for regions 12:109639296 & 15:51201293 from Who...
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Vempalli Fazulur commented,
Dear Genevieve, Thanks a lot for providing the resources to troubleshoot the issue. I tried running Mutect2 with options --debug, --linked-de-bruijn-graph, --bam-output & --recover-all-dangling-bra...