Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Doubts regarding samtools mpileup - Call somatic mutations from a pair of samples ?

    I am trying to compare two samples for somatic mutations using Samtools mpileup. (RNAseq data)


    The two .bam files or samples I am comparing include multiple samples merged together into them (3 .bam files in one and 8 in other- merged using samtools merge)

    The command given in the manual
    ( " samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair - > var.bcf" ) doesnt specify the number of samples (inputs)

    I used this command

    samtools mpileup -DSuf ref.fa aln1.bam aln2.bam | bcftools view -bvcgT pair - > var.bcf

    It gives me back the error saying
    "[mpileup] 1 samples in 2 input files
    <mpileup> Set max per-file depth to 8000
    [afs] 0:0.000"

    I also tried to make a sample.txt file for the two samples (merged files) and used this command

    "samtools mpileup -DSuf ref.fa aln1.bam aln2.bam | bcftools view -bvcgT pair -s samples.txt - > var.bcf "

    I still get an error (different error)

    Is there anything wrong here ?

    What should be the ideal steps to find out somatic variants between two samples ? (samples include multiple bam files merged together)

    Please suggest me some steps to be followed in order to find out somatic variants by comparing two samples using samtools mpileup

    Thanks!

  • #2
    Originally posted by swapnil2188 View Post
    I am trying to compare two samples for somatic mutations using Samtools mpileup. (RNAseq data)


    The two .bam files or samples I am comparing include multiple samples merged together into them (3 .bam files in one and 8 in other- merged using samtools merge)

    The command given in the manual
    ( " samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair - > var.bcf" ) doesnt specify the number of samples (inputs)

    I used this command

    samtools mpileup -DSuf ref.fa aln1.bam aln2.bam | bcftools view -bvcgT pair - > var.bcf

    It gives me back the error saying
    "[mpileup] 1 samples in 2 input files
    <mpileup> Set max per-file depth to 8000
    [afs] 0:0.000"

    I also tried to make a sample.txt file for the two samples (merged files) and used this command

    "samtools mpileup -DSuf ref.fa aln1.bam aln2.bam | bcftools view -bvcgT pair -s samples.txt - > var.bcf "

    I still get an error (different error)

    Is there anything wrong here ?

    What should be the ideal steps to find out somatic variants between two samples ? (samples include multiple bam files merged together)

    Please suggest me some steps to be followed in order to find out somatic variants by comparing two samples using samtools mpileup

    Thanks!
    Please can Anyone help me with this ?

    I am waiting for response !

    Thank You !

    Comment


    • #3
      Do you have read group information specified in the two files?

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Current Approaches to Protein Sequencing
        by seqadmin


        Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
        04-04-2024, 04:25 PM
      • 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

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 04-11-2024, 12:08 PM
      0 responses
      34 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 10:19 PM
      0 responses
      37 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 09:21 AM
      0 responses
      31 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-04-2024, 09:00 AM
      0 responses
      54 views
      0 likes
      Last Post seqadmin  
      Working...
      X