User: Mehulsharma.253

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Posts by Mehulsharma.253

<prev • 22 results • page 1 of 3 • next >
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Mate mismatch errors in 1000genomes CRAM files
... I downloaded some CRAM files for variant calling from the [1000 genomes FTP server][1]. I also downloaded the reference genome and MD5 cache as per the instructions in this [README doc][2]. However, running Picard tools' *ValidateSAMfile* gave errors (refer below) in both the CRAM as well as the s ...
validatesam 1000genomes fixmate matepairs cram written 6 months ago by Mehulsharma.25310
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Comment: C: Convert specific regions in bam file to vcf and annotating the vcf
... This link doesn't work ...
written 7 months ago by Mehulsharma.25310
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Comment: C: How to choose good tools for identifying functional SNPs?
... what tools would you recommend to asses the effect of variants on ligand binding ?Schrodinger maestro seems good but it's a paid software. ...
written 7 months ago by Mehulsharma.25310
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CRAM reference registry and the GRch38 reference genome
... Hi. I'm downloading some CRAM files from 1000genomes for use in variant calling. I will convert them to BAM (since most tools can't call from CRAM files). I'm a bit confused about how to go about this process since I assumed a straightforward Samtools based conversion based on a given reference FAST ...
cram bam samtools variantcalling grch38 written 7 months ago by Mehulsharma.25310 • updated 7 months ago by h.mon26k
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Dealing with a large sample for variant calling
... I have a large number of samples. Like a 100 samples at least (plus these are paired end reads). I aim to call variants on these samples and then predict their effects on protein structure dynamics. The only way that seems possible for now is to align each sample individually, pre-process them ind ...
jointcalling ngs alignment variantcalling written 7 months ago by Mehulsharma.25310 • updated 7 months ago by Pierre Lindenbaum121k
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Comment: C: Bash vs WDL for running GATK
... Thank you ! Pardon me if the question sounds dumb but what would be the difference vis a vis just piping commands together in a bash shell using the standard tools-specific commands ? What would be the primary advantage of a WDL script / Cromwell engine in that aspect ? Does it streamline my process ...
written 7 months ago by Mehulsharma.25310
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Effect of dbSNP build differences in variant calling
... I want to call variants on prealigned CRAM files for a 1000genomes sample, available for download. However, the dbSNP build used to recalibrate base quality scores (the dataset is already recalibrated) for all 1000genomes phase 3 pipelines is dbSNP build 142 which is the 2014 version (current build ...
assembly grch38 dbsnp variantcalling gatk written 7 months ago by Mehulsharma.25310
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Comment: C: GATK best practices for Broad-produced NGS data
... Thank you ! GATK forums seems to be having some issues with enabling posting and commenting because of recent spam reports but I will retry posting there. ...
written 7 months ago by Mehulsharma.25310
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GATK best practices for Broad-produced NGS data
... This is a more generalised question. I wish to discover variants in my raw WGS data which has been produced by studies carried out by Broad Institute. What modifications would you recommend for the standard GATK best practices workflow to better suit Broad-produced data ? For e.g., while GATK/Broa ...
gatk4 ngs broadinstitute variantcalling written 7 months ago by Mehulsharma.25310 • updated 7 months ago by vdauwera940
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Warning in GATK Picard MarkDuplicates
... I ran MarkDuplicates on my sorted BAM file with GATK 4.0.11 picard tools but got the following warning: > WARNING 2018-12-07 > 10:14:23 AbstractOpticalDuplicateFinderCommandLineProgram A field > field parsed out of a read name was expected to contain an integer and > did not. Read name ...
variant calling gatk picard markduplicates written 7 months ago by Mehulsharma.25310 • updated 7 months ago by Pierre Lindenbaum121k

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Scholar 7 months ago, created an answer that has been accepted. For A: Setting temporary directory for GATK4 SortSam

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