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• Bowtie2 hg19 reference for gatk MuTect
  Hello, I understand that the suggested aligner to use with GATK is bwa. If I want to use Bowtie2 ...
• Confusion with High Confidence SNP Calls (Overlap B/w RNA-seq & WGBS calls) and Genome Assemblies Used for Alignment and Annotation
  Hi! Here is what I have, I have SNP calls from RNA-Seq (paired end) and SNP calls from WGBS perf...
• Indexing reference genome for GATK
  I have created .bam files using BWA and Samtools having downloaded a reference genome hg19 from U...
• calling the variants in a sample with respect to other sample
  I have two different samples, say **WT (wildtype)** and **A6 (Crispr mutated)**. (samples are il...
• Using Gatk On Inbred Species - What To Do With The Heterozygous Calls?
  Does anyone here have experience using GATK for SNP and indel calling on an inbred species? Do y...
• Ensembl Genome annotations versions
  I am running a GATK pipeline on RNA-seq data. For the alignment I have used GATK-bunle genome - h...
• SNP calling from pooled RNA-seq data
  Hello, I want to call SNPs from pooled RNA-seq data that have been mapped to a reference genome....
• Need Help With The Gatk Usage
  I have some more query for which I need some suggestions, I am new to GATK and want to use it for...
• Best Human Genome Reference File For Gatk?
  On GATK website http://gatkforums.broadinstitute.org/discussion/1204/what-input-files-does-the-ga...
• Skipping The Local Realignment Around The Indels And Rather Aligning The Mapped Reads On The Exonic Region.
  I have a query that we do the local realignment around the indels with the known sites because it...
• can variants be called between two genomes?
  Usually, SNP calling is between a reference genome sequence (fasta) and reads (fastq), is it po...
• Can Anyone Suggest Me A Script Based Pipeline For Exome Sequencing With Paired End Reads Generated By Illumina For Tumor Samples.
  Can anyone suggest me a pipeline with scripts for exome sequencing starting from the raw reads(p...
• Using Tophat2 to align illumina files to ucsc hg19
  Hello, I need to use Tophat2 to align RNAseq from 16 tissues (downloaded from the European Nucleo...
• Updated Alignment of current refseq transcripts against hg19
  I am in search for an alignment file of up to date (latest release is 92 from January 2019) refse...
• Variant calling within and between 2 nematode strains
  Dear all, I have the genome sequence of a nematode species I'm working with. This genome was ass...
• snpEff database to annotate b37 GATK output
  Anyone uses SnpEff to annotate GATK output? After downloading the newest snpEff (03/29/2017), I f...
• How do I get the unique SNPs for each strain?
  Hi, First, I would like to say that I'm new to genome and variant calling data analyses and, of...
• Why does inclusion of decoy sequences cause more BWA alignments to an autosome?
  I am seeing strange behavior when comparing alignments generated by bwa mem 0.7.12 to two differe...
• Gatk Unifiedgenotyper Error:Error: The Number Of Base Qualities Does Not Match The Number Of Bases In M_Solexa-Ga04_Jk_Pe_Sl19_Repeat:6:56:1719:1324
  Hi all, When I used GATK UnifiedGenotyper to call variants from three Neanderthal BAM files, the...