User: gprashant17

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gprashant1770
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Posts by gprashant17

<prev • 25 results • page 1 of 3 • next >
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Filtering specific columns (SAMPLE IDs) in a VCF file using BCFtools
... I would like to filter variants from a VCF file for only specific samples. I have a file (sample_file.txt) that contains a single column of the required Sample IDs. I used this command: ./bcftools view --force-samples sample_file.txt file.vcf > output.vcf But I get this error: &g ...
vcf software error bcf snp rna-seq written 5 hours ago by gprashant1770
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Comment: C: Filtering out by gene and samples from VCF files
... Thanks, filtering out based on the samples (individuals) can be done in the same manner? ...
written 5 weeks ago by gprashant1770
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Filtering out by gene and samples from VCF files
... Hi, I have a set of genes and samples from GTEx dataset. I want to filter out variants from a very large VCF file corresponding to these genes and samples. Is there any way to implement the same using VCFtools? Thanks ...
vcf gene snp vcftools gtex written 5 weeks ago by gprashant1770 • updated 5 weeks ago by Pierre Lindenbaum124k
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Comment: C: Filtering significant somatic variants from a VCF file
... I have aligned RNA-seq tumour samples using STAR and I am following GATK's best practices for variant calling, in order to identify somatic mutations causing cancer. Since I do not have a normal sample, I used Mutect2 with only the required arguments. I am encountering these filters (PASS, Clustere ...
written 5 months ago by gprashant1770
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Filtering significant somatic variants from a VCF file
... I have used GATK's pipeline (RNA-seq alignment) and obtained a VCF file using Mutect2 and FilterMutectCalls. Filters such as PASS, Clustered_events, germline, weak-evidence, etc. were added to the variants. Before annotating the file with dbSNP, COSMIC, ANNOVAR, I would like to filter out significan ...
vcf ngs alignment rna-seq mutations written 5 months ago by gprashant1770
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Where can find we find dbSNP database for Human Genome GRCh38.p12
... In the FTP website of dbSNP, I am able to find the latest releases for the human genome GRCh38.p13 and also for GRCh38.p7 in the archives. But I am using GRCh38.p12 for RNA-seq alignment. Is it fine to use the database corresponding to p7 or is there any way I can obtain the database for p12? ...
vcf alignment dbsnp snp rna-seq written 5 months ago by gprashant1770 • updated 5 months ago by Bastien Hervé4.5k
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How to create a mutation landscape from a VCF file?
... I have a VCF file which I have obtained from an aligned BAM file, and I want to identify somatic mutations. I would like to create a mutation landscape so that I can easily compare with databases like dbSNP, COSMIC, etc. Is there a way to do this? Or is there any other way I can use my VCF file to ...
vcf genome snp rna-seq written 5 months ago by gprashant1770
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Reference Index and Feature Index not matching while using BaseRecalibrator
... I have downloaded the databases for dbSNP and COSMIC in order to use the BaseRecalibrator tool in GATK, which has an option called --known-sites. The reference genome I use in GRCh38.p12 from GENCODE (latest version). However, it looks like the indices in my reference genome are "chr1, chr2, chr3 .. ...
gatk ngs alignment snp rna-seq written 5 months ago by gprashant1770
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Comment: C: Empty VCF files produced by both Mutect2 and HaplotypeCaller?
... I'm not sure which output should I post. The command ran with no errors. It showed ProgressMeter for all the traversals and ended like this: 17:39:21.868 INFO ProgressMeter - Traversal complete. Processed 10840980 total regions in 19.1 minutes. 17:39:21.915 INFO VectorLoglessPairHMM - Tim ...
written 5 months ago by gprashant1770 • updated 5 months ago by RamRS25k
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Comment: C: Empty VCF files produced by both Mutect2 and HaplotypeCaller?
... Yes, I am able to view the bam files using samtools. I should mention here that I have used AddOrReplaceReadGroups (GATK) to include the @RG tag in the header, as it was not present initially. ...
written 5 months ago by gprashant1770

Latest awards to gprashant17

Student 6 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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