User: gprashant17

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gprashant1770
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Posts by gprashant17

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Empty VCF files produced by both Mutect2 and HaplotypeCaller?
... I have tried using both Mutect2 and HaplotypeCaller (GATK) for calling somatic variants and generating VCF file from an aligned BAM file (RNA-seq). However, the generated VCF file did not have any information other than the header. I have seen this type of thread online, but I did not manage to find ...
snp rna-seq haplotype-caller mutect sequencing written 7 months ago by gprashant1770 • updated 5 months ago by Biostar ♦♦ 20
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Comment: C: MarkDuplicates output file in GATK pipeline
... So if I did not use --REMOVE_DUPLICATES, the duplicate reads will still be present in the marked_duplicates.bam but they would have been flagged as duplicates right? ...
written 7 months ago by gprashant1770
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MarkDuplicates output file in GATK pipeline
... I have used GATK's MarkDuplicates on a BAM file I obtained after alignment, which resulted in another file marked_duplicates.bam. So should I proceed with this marked_duplicates.bam file for analysis (converting to VCF), or this is just a file containing duplicates? In the latter case, is it possibl ...
gatk alignment bam rna-seq sequencing written 7 months ago by gprashant1770 • updated 7 months ago by Pierre Lindenbaum125k
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Comment: C: What are the best set of options to use while aligning using STAR?
... Thanks, I would like to separate the mapped and unmapped reads into two different SAM/BAM files and I did not notice a way to do that in the manual. Is there any other way or including the unmapped reads within the same alignment file is the only option? ...
written 7 months ago by gprashant1770
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Comment: C: What are the best set of options to use while aligning using STAR?
... I just tried using --chimSegmentMin 20 --chimOutType WithinBAM. Most of my reads are 2*101 base pairs long and the minimum is around 40 (for one mate). I used WithinBAM option as that would allow me to use another option --peOverlapNbases, for detecting overlapping within read pairs. As this would ...
written 7 months ago by gprashant1770
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Comment: C: What are the best tools for analyzing and identifying somatic mutations?
... Using a few of them and comparing the results would work I guess, thanks. ...
written 7 months ago by gprashant1770
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What are the best set of options to use while aligning using STAR?
... Hi, I have a tumour RNA-seq data, which I have aligned using STAR with a human reference genome, using the basic default options. However, I am confused with the variety of options (chimeric junctions, 2-pass mapping, readCounts, etc) available in the STAR manual and I would like to know which of th ...
ngs alignment star rna-seq written 7 months ago by gprashant1770 • updated 7 months ago by Charles Warden7.5k
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What are the best tools for analyzing and identifying somatic mutations?
... Hi, I am looking for tools to identify somatic mutations (SNPs, CNVs, indels, etc) from a tumour sample (RNA-seq) which has been aligned with the human reference genome using STAR. I noticed that there are many tools (MuTect, MuSE, VarDict, etc) for generating a vcf file. It looks like these tools r ...
vcf bam snp rna-seq sam written 7 months ago by gprashant1770 • updated 7 months ago by ATpoint28k
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Comment: C: Usage of Mutect2
... Since I do not have the data for any normal tissue from the same human, is there a way to skip this step? ...
written 7 months ago by gprashant1770
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Usage of Mutect2
... Hi, I have been trying to use the Mutect2 of GATK toolkit, and noticed an example usage: java -jar GenomeAnalysisTK.jar \ -T MuTect2 \ -R reference.fasta \ -I:tumor tumor.bam \ -I:normal normal.bam \ [--dbsnp dbSNP.vcf] \ [--cosmic COSMIC.vcf] \ [-L targets.in ...
gatk next-gen snp rna-seq mutect2 written 7 months ago by gprashant1770 • updated 7 months ago by MatthewP390

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Student 7 months ago, asked a question with at least 3 up-votes. For What are the best set of options to use while aligning using STAR?

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