User: Mehulsharma.253

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Posts by Mehulsharma.253

<prev • 19 results • page 1 of 2 • next >
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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 14 hours ago by Mehulsharma.25310 • updated 8 hours ago by h.mon21k
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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 3 days ago by Mehulsharma.25310 • updated 3 days ago by Pierre Lindenbaum115k
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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 3 days 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 5 days 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 5 days 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 5 days ago by Mehulsharma.25310 • updated 5 days ago by vdauwera890
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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 8 days ago by Mehulsharma.25310 • updated 8 days ago by Pierre Lindenbaum115k
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Answer: A: Out Of Disk Space With Picard Tools ?
... The problem is, as others said with a probable low space in the default temporary directory. I changed my directory to a custom one. Worked perfectly for me using this code: ./gatk --java-options "-Djava.io.tmpdir=/custom file path" SortSam -I=samplealn.sam -O=sortedsamplealn.bam -SO=coordinat ...
written 8 days ago by Mehulsharma.25310
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Answer: A: Temporary Directory Problem in GATK4
... My problem was resolved using: ./gatk --java-options "-Djava.io.tmpdir=/custom file path" SortSam -I=samplealn.sam -O=sortedsamplealn.bam -SO=coordinate --TMP_DIR=/custom file path ...
written 8 days ago by Mehulsharma.25310
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Answer: A: Setting temporary directory for GATK4 SortSam
... I got it using ./gatk --java-options "-Djava.io.tmpdir=/custom file path" SortSam -I=samplealn.sam -O=sortedsamplealn.bam -SO=coordinate --TMP_DIR=/custom file path ...
written 8 days ago by Mehulsharma.25310

Latest awards to Mehulsharma.253

Scholar 8 days ago, created an answer that has been accepted. For A: Setting temporary directory for GATK4 SortSam

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