Similar posts • Search »

• Varscan variant calll error on pacbio data
  Hello I'm trying to call variants on an alignment of pacbio data to a reference thusly: bl...
• samtools mpileup - how to extract the alternative allele counts for *each* alternative base
  Hello there I am running samtools mpileup and get an output for the requested positions. My prob...
• How best to parse samtools mpileup results?
  I am trying to characterize the depth of coverage for SNPs/INDELs/other variants in my BAM/SAM fi...
• Why there is huge difference in mapping quality with bwa & bowtie
  Hie NGS Geeks, Recently I observed some huge difference in mapping quality when aligned with bow...
• Understanding Mpileup Alternate Allele Coding
  Hi, I am trying to count all the bases found at a specific site within a bam file using the foll...
• Mpileup BCF/VCF output without non-ref base 'X'?
  Hi - I am obtaining from a RNA-seq bam file the BCF output from samtools mpileup in order to corr...
• Get All Alleles Of 1 Column In Bam File
  Hi all, I have bam files from which I would like to extract 1 specific column (ie chr:position). ...
• Samtools : what is threshold for the mapping quality?
  Hie friends, I am new to samtools, however I used samtools for calling variants for study and I ...
• Output AO using bcftools
  I calling variants from sorted bam files using `samtools mpileup` and then `bcftools call -cv inp...
• samtools mpileup: how to output qname (read id) along with other information
  Dear All, I use samtools mpileup as following samtools mpileup -O -r chr1:10915996-10915996 E13...
• Parsing Base String From Samtools Mpileup
  Hello everyone, I am trying to construct B-allele frequency plots from NGS data; and for that I ...
• Mutect Allele Counts Vs Mpileup
  Hi everyone, I used Mutect to call somatic mutations in my exome sequencing experiment. Just to...
• Output all allele counts at each position using bcftools
  Hello, I have a bam file and would like to know all different allele counts at every position - ...
• Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
  Hi everyone, I have a number of Human Heart RNASeq samples. I have generated a mpileup file on e...
• Tetraploid Snp Calling & Snp Filtering
  Dear all, I'm currently working on a project involving SNP calling of resistance genes (R-genes)...
• Samtools mpileup quality scores all zero
  Hi everyone. I'm calling some variants using samtools (and bcftools) from a bwa aligned and sort...
• Specific output from bcftools, difference between DP4 and AC scores
  Hi all! I'm new to SNP calling, trying to call multisample data and output SNP counts for every o...
• Varscan output contains dots
  Hi guys, I'm using VarScan v 2.3.7 to call SNPs in Illumina Hiseq2000 RNA-Seq paired-end sample:...
• Count References Read From Bam File
  I want to know how many reads (above certain score ) supporting References allele at each positio...
• Difference In Quality Strings For Samtools Mpileup When Using -L Option Versus -R Option
  Hello - I was wondering if anyone else has noticed this wierd phenomena using the Samtools mpil...