how to find snp changes between pairs of samples that have genomes sequenced

Question

[bryanchang2016]

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.

[GenoMax]

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.

[bryanchang2016]

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)?

[GenoMax]

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

[bryanchang2016]

here is the link to the database