User: sktbanerjee1

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sktbanerjee130
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Posts by sktbanerjee1

<prev • 11 results • page 1 of 2 • next >
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representation of chromosomal positions in the format of cytogenetic band.
... Hello, I have some variants in standard vcf format. I want to represent them in [chromosome no][arm name] [band position] based location. is there any way i can convert my positions in this format using some tool. Thanks in advance. ...
chromosomal position variant representation. written 12 months ago by sktbanerjee130 • updated 12 months ago by Pierre Lindenbaum107k
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I need some sets of pathogenic variants related to any mendelian disorder.
... Hello everyone, I am working on a method to prioritize pathogenic variants from exome sequencing data. I have developed a method, but how to validate that? where will i be able to get a set of pathogenic variants so that I can check the efficiency of our method? ...
prioritization variant written 12 months ago by sktbanerjee130 • updated 12 months ago by WouterDeCoster28k
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converting wannovar generated csv annotation data to a vcf=4.1 file.
... hello everyone. so, I have called somatic variants using GATK Mutect2 for tumor normal samples, and then annotated them with the web version of annnovar available, and after the annotation procedure I got a .csv file. now I want to convert that .csv file into a conventional vcf file for variant prio ...
vcf csv wannovar variant prioritization written 12 months ago by sktbanerjee130
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Comment: A: Somatic variant call
... Thanks for all your replies. ...
written 13 months ago by sktbanerjee130
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Comment: C: Somatic variant call
... Thanks for the reply. I have annotated the variants generated by Mutect2 using web version of Annovar, and I am planning to do the same with my variants generated by varscan. But, the number of variants in the varscan output is my real cause of worry. ...
written 13 months ago by sktbanerjee130
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Somatic variant call
... I have matched samples from three tissues of an individual and I am trying to prioritize the pathogenic variants depending upon phenotype terms encoded by HPO. For my variant calling I have used Mutect2, and Varscan v2.3.9. but none of the called somatic variants from both the tools are common, and ...
varscan2.3.9 somatic mutect2 snp variat-filtering written 13 months ago by sktbanerjee130 • updated 4 months ago by liangqinsi20
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Comment: C: Obtaining read group information from the Fastq file
... Thanks a lot for your replies. ...
written 14 months ago by sktbanerjee130
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Comment: C: Obtaining read group information from the Fastq file
... Thanks, for the help. I was wondering if including the read group information in the bwa-mem step would fix this? If, Yes, then how to find out the read group information. ...
written 14 months ago by sktbanerjee130
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Is it necessery to perform GATK-BQSR before performing variant calling using freebayes.
... I am trying to call variants from whole exome paired end sequences aligned to HG38p7 using the Freebayes variant caller. As it is a general recommendation to perform BQSR before any type of variant calling, I was wondering is it necessary to perform the BQSR before calling variants with freebayes? ...
gatk bqsr freebayes written 14 months ago by sktbanerjee130 • updated 14 months ago by finswimmer2.0k
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Comment: A: Obtaining read group information from the Fastq file
... Actually, after QC I have aligned them using BWA-MEM. now I am to call variants using GATK haplotype caller, but before that I am to re calibrate the base quality scores using GATK BQSR. when I try to perform that task, I get an error "ERROR: ReadGroup information in the BAM header is not present". ...
written 14 months ago by sktbanerjee130

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