Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Jeremy
    replied
    You could try a different SNP calling program like freebayes or gatk.

    Leave a comment:


  • swbarnes2
    replied
    Strange. One suggestion...try

    samtools mpileup -Buf my.fa my.bam | bcftools view -vcg
    The -B turns off BAQ recalculation..I've gotten strange results when it was on, which were repaired by turning it off.

    Leave a comment:


  • maivantan
    replied
    2. output of bcftools (looks heterozygous to me):
    chrX 2779570 . A G 99 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,0,35,5;MQ=60 PL:GT:GQ 255,120,255:0/1:99

    I think this is heterozygous SNP, you can see this values 0/1:99

    Leave a comment:


  • biomichael
    replied
    This is surely a heterozygos SNP site from A to G

    Leave a comment:


  • idyll_ty
    replied
    Have you solved this problem? I also have this problem, and I'm very interested in the result.

    Originally posted by grievous View Post
    Hi all,

    I'm new to SNP-calling with mpileup/bcftools. After my first analysis it seems to me, that I cannot properly call homozygous SNPs...

    whole command (samtools-0.1.16):
    samtools mpileup -uf my.fa my.bam | bcftools view -vcg -

    1. output of mpileup (here in pileup-format, looks homozygous to me -> G?!):
    chrX 2779570 A 41 GGGGGGGGGGGGGGgGgGGGGGGGGGgGGgGGGGgGGGGGg I<FHIIBEB?FIIIIEGGHIIIGHGDGIHDBIGIH=IIIH#

    2. output of bcftools (looks heterozygous to me):
    chrX 2779570 . A G 99 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,0,35,5;MQ=60 PL:GT:GQ 255,120,255:0/1:99

    Can anyone tell me the reason for this behaviour?
    Thank you.

    Leave a comment:


  • grievous
    started a topic mpileup and homozygous snps

    mpileup and homozygous snps

    Hi all,

    I'm new to SNP-calling with mpileup/bcftools. After my first analysis it seems to me, that I cannot properly call homozygous SNPs...

    whole command (samtools-0.1.16):
    samtools mpileup -uf my.fa my.bam | bcftools view -vcg -

    1. output of mpileup (here in pileup-format, looks homozygous to me -> G?!):
    chrX 2779570 A 41 GGGGGGGGGGGGGGgGgGGGGGGGGGgGGgGGGGgGGGGGg I<FHIIBEB?FIIIIEGGHIIIGHGDGIHDBIGIH=IIIH#

    2. output of bcftools (looks heterozygous to me):
    chrX 2779570 . A G 99 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,0,35,5;MQ=60 PL:GT:GQ 255,120,255:0/1:99

    Can anyone tell me the reason for this behaviour?
    Thank you.
    Last edited by grievous; 06-19-2011, 10:46 AM.

Latest Articles

Collapse

  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    04-22-2024, 07:01 AM
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 08:47 AM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
60 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
59 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
54 views
0 likes
Last Post seqadmin  
Working...
X