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• What is the best way to make a bam file smaller by removing unwanted information?
  Hi!  I am trying to make smaller many BAM files (around 60 of them) of size ~200GB (due to disk ...
• Variant calling: Samtools QUAL from NGS data Vs. Sanger quality score
  So I've sequenced samples with MinION NGS platform, and analysed for SNPs via SAMtools/BCFtools. ...
• (samtools) Filtering and interpreting >100 QUAL scores
  I am in the process of filtering/selecting variants via samtools/bcftools for sample RNA sequence...
• Need help understanding read depth for somaticsniper vcf's
  Hi, I'm having trouble understanding read depth in vcf's called by somatic-sniper. Here is a sa...
• Should I use reads with good quality but failed-vendor flag?
  Hi guys, Quick question is: I have some mapped reads in bam file which have good read quality, b...
• bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
  I'm running bbmap's callvariants.sh this way for a diploid population of several samples: ca...
• Vcf File Format Qual Column
  I'm generating a VCF file which consists of genotype data from 5 individuals. For each variant fr...
• Variants calling (VCF)
  I am new to ngs data analysis. I have the VCF file from targeted sequencing of 3 genes. How can i...
• Snp Calling - Filter Reads According To Quality Of 5 Flanking Bases
  Hi, I am trying to detect low level variants (minor allele present at min 10%). I am using sever...
• Interpretting QUAL/DP4 in VCF files
  I need some help in interpreting what the QUAL and DP4 in VCF files mean. So from what I understa...
• Samtools mpileup quality scores all zero
  Hi everyone. I'm calling some variants using samtools (and bcftools) from a bwa aligned and sort...
• Why Does Samtools/Bcftools Give Incorrect Genotypes And Innacurate Quality Scores?
  I have resequenced a target region in depth and called with samtools with default parameters (exc...
• Variant calling on bacterial population using Freebayes gave wrong allele frequency and extremely low QUAL
  I am working on genomic data of 8 evolving bacterial populations. Each one of them is a communi...
• How To Convert And Filter Scf Format Into Fasta?
  If I have a large number of files in SCF format, and want to batch convert them into Fasta format...
• Qual Versus Bq Tag In Sam/Bam
  I've noticed in many of the 1000genome BAMs there are qual strings (Phred), one per base, giving ...
• Is It Necessary To Do Base Quality Score Recalibration Before Variants Detection In Gatk
  Hi, As it mentioned in here, the reported base quality scores (the QUAL column in BAM file) befo...
• Mapping Quality Scale Filtering
  I have a highly repetitive, 3x versions of chromosome containing reference with a great deal of s...
• How to set up quality filter which only applies to the 5' end of reads
  Hi, All, I have a question of how to set up a quality filter which only applies to the first 3 b...
• Filtering Strategy In Exome Sequencing And Quality Control
  To filter exome sequence data and remove false positive I know read depth and Phred score are rou...
• How To Select The Top 30% Variants (Based On Quality) From A Vcf File?
  How can I select the top 30% variants (based on quality) from a VCF file? So all the the varia...