User: sktbanerjee1

gravatar for sktbanerjee1
sktbanerjee120
Reputation:
20
Status:
New User
Location:
Last seen:
2 months ago
Joined:
7 months, 1 week ago
Email:
s***********@gmail.com

Posts by sktbanerjee1

<prev • 11 results • page 1 of 2 • next >
5
votes
1
answer
138
views
5 follow
1
answer
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 3 months ago by sktbanerjee120 • updated 3 months ago by Pierre Lindenbaum96k
0
votes
1
answer
139
views
1
answer
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 3 months ago by sktbanerjee120 • updated 3 months ago by WouterDeCoster20k
0
votes
0
answers
163
views
0
answers
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 3 months ago by sktbanerjee120
0
votes
0
answers
234
views
0
answers
Comment: A: Somatic variant call
... Thanks for all your replies. ...
written 4 months ago by sktbanerjee120
0
votes
0
answers
234
views
0
answers
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 4 months ago by sktbanerjee120
0
votes
0
answers
234
views
6 follow
0
answers
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 4 months ago by sktbanerjee120
0
votes
1
answer
294
views
1
answers
Comment: C: Obtaining read group information from the Fastq file
... Thanks a lot for your replies. ...
written 4 months ago by sktbanerjee120
0
votes
1
answer
294
views
1
answers
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 5 months ago by sktbanerjee120
1
vote
1
answer
228
views
1
answer
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 5 months ago by sktbanerjee120 • updated 5 months ago by finswimmer360
0
votes
1
answer
294
views
1
answers
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 5 months ago by sktbanerjee120

Latest awards to sktbanerjee1

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 452 users visited in the last hour