RaviKumarSindhu ✭

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• Hi, I am working with Human sample WGS data (30X, PE reads, HiSeq platform) and facing problem at VQSR and variant annotation step. I ran following commands (modified here, path deleted) to get my files: * Converted each sample's bam file into …

  in Variant Quality Score Recalibration (VQSR) Comment by RaviKumarSindhu January 2017
• "Gzipped fasta files will not work with the GATK, so please make sure to unzip them first."

  in (howto) Prepare a reference for use with BWA and GATK Comment by RaviKumarSindhu August 2016
• Hi, I have a question about index of human reference genome using BWA. Is it ok to index the "zipped" fasta file of Human reference genome or one should ist unzip it and then index it using BWA ?. (1). bwa index -a bwtsw human_g1k_v37.fasta.gz …

  in (howto) Prepare a reference for use with BWA and GATK Comment by RaviKumarSindhu July 2016
• Hi Geraldine, Thank you for the response. Now i am sure that i didn't have open access/permission of these FTP sites as mentioned by you and Ms. Sheila. Whenever i clicked these links or copy n paste them as new URL, the link eventually turn into…

  in Questions about the resource bundle (continued) Comment by RaviKumarSindhu July 2015
• Hi Sheila, Thank you for the response. Ah...i am sure i am missing some information as i want to use my browser as FTP client, but i haven't change any settings therefore it is taking me to general broadinstitute FTP (ftp://ftp.broadinstitute.org…

  in Questions about the resource bundle (continued) Comment by RaviKumarSindhu July 2015
• Hello Geraldine, I am looking for bundle (having human reference genome hg19) but i didn't get it. The working link is taking me to "ftp://ftp.broadinstitute.org/" where there are number of directories e.g. Parent Directory distribution …

  in Questions about the resource bundle (continued) Comment by RaviKumarSindhu July 2015