Question: how to find snp changes between pairs of samples that have genomes sequenced
0
gravatar for bryanchang2016
7 weeks ago by
bryanchang201610 wrote:

Hi everyone I'm new to bioinformatics and I want to identify significant snp changes between pairs of samples (patient isolates that are resistant and non-resistant to fluconazole) of cryptococcus neoformans which have had their genomes sequenced and [put on ebi database[1] I've tried looking for a way to do this on fungidb but am unable to find the right tool. Would anybody be able to give me some advice on how to proceed? Thanks.

variant genome • 163 views
ADD COMMENTlink written 7 weeks ago by bryanchang201610
1

Here is an outline of what you can do:

  1. Get original fastq sequence for samples from EBI
  2. Get reference genome sequence for Cryptococcus neoformans.
  3. Index the genome with an aligner of your choice (bwa, bowtie2, bbmap etc)
  4. Align your samples to the reference.
  5. Sort/index alignment files.
  6. Call variants on the two alignments
  7. Use bcftools isec to find changes that are sample specific.
ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by genomax89k

I have compared each sample to reference on veupathdb and have obtained vcf files for each sample. But is there a way I can do bcftool on veupathdb/fungidb to find changes between two vcf files (resistant/nonresistant)?

ADD REPLYlink written 7 weeks ago by bryanchang201610

If the VCF files are called against an identical reference then use: A: How bcftools isec works ?

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by genomax89k

here is the link to the database

ADD REPLYlink written 7 weeks ago by bryanchang201610
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1636 users visited in the last hour