Question: 8 column output file from SAMtools mpileup
gravatar for ersniels
4.3 years ago by
ersniels0 wrote:

Hi all,

First let me briefly describe what I am trying to do. I have Illumina reads (ezRAD and Illumina MiSeq), from which I want to identify putative neutral and adaptive SNPs. Here's what I have done so far:

  • trimmed the reads for adaptors and quality with FASTQC toolkit
  • inported the reads into GALAXY
  • groomed the reads so that they were converted from phred+64 to phred+33
  • mapped these reads onto my reference genome (L. gigantea) with BWA-MEM with default parameters
  • cleaned the output BAM files with CleanSAM in SAMtools using the strict option
  • filtered the BAM files to remove alignments with MAPQ < 15, using Filter SAM tool under SAMtools in Galaxy
  • Merged my BAM files so all of my samples were combined, using merge BAM tool under SAMtools in Galaxy, with default parameters
  • performed an Mpileup on the merged BAM file using SAMtools, where I did not perform genotype likelihood computation, with the same reference genome and basic parameters

After performing the Mpileup, I got a pileup output file that looks like this (only showing the 1st two lines):

1 2 3 4 5 6 7 8

LOTGIsca_18122 322 T 0 185

LOTGIsca_18122 323 A 0 186

Now I am very confused, as I thought pileup output files were either 5 or 10 columns, and I have 8... Also, I tried to filter the pileup output file with VARSCAN, using default parameters, and I get an output file with 0 lines.

Any input on what I have done, or what I should rather do instead would be greatly appreciated.

Thanks! Erica

snp next-gen • 1.3k views
ADD COMMENTlink modified 2.1 years ago by Biostar ♦♦ 20 • written 4.3 years ago by ersniels0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 800 users visited in the last hour