Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • filtering mpileup results

    Does anyone have any suggestions on filtering the mpileup results? We have obtained SNPs/indels according to the command lines on the mpileup website:

    samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf (1)
    bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf (2)

    As in pileup where there is "awk '($3=="*"&&$6>=50)||($3!="*"&&$6>=20)' sample1.flt.txt > sample1.final.txt" suggested to filter the results, are there similar rules necessary to filter mpileup results?

    For example, is the 6th column (named QUAL) in the vcf file from (2) the same as the 6th column in the pileup file, and is it appropriate to apply "$6>20" for the vcf file too?

    Any suggestion is appreciated.

  • #2
    If you only have one sample in your vcf, filtering on depth might be more useful. You can use the DP value, but the DP4 values will omit poor quality reads, which probably makes it more useful. But it's a trickier awk statement.

    If you have multiple sample, QUAL won't help you figure out which samples really have the SNP, and which don't. The best you can do is to use the GQ quality, and unfortunately, you won't have depths of coverage for individual samples.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 03-27-2024, 06:37 PM
    0 responses
    13 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-27-2024, 06:07 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    53 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    69 views
    0 likes
    Last Post seqadmin  
    Working...
    X