extract SNP, variants

Question

[bruseq]

Hello everyone,

Is there any tool or command to find out SNP, indels, genome coverage, X-coverage from .bam file.

Thanks, Divya

[Buffo]

Samtools :) mpileup mainly

http://www.htslib.org/doc/samtools.html

[Matteo Schiavinato]

Samtools mpileup | bcftools call

https://samtools.github.io/bcftools/bcftools.html

[WouterDeCoster]

That's quite a lot of questions in one sentence. You mean you still have to do variant calling?

[ivivek_ngs]

wow you have the entire exome/WGS analysis fishing SNVs or MNVs in one question. Congrats! Take simple cues and rephrase and read papers.

1. What kind of data do you have?

2. How did you generate bam files?

3. If exome data/whole-genome you should see GATK and all your queries will be answered and then once you learn it you can use other tools to make your results more strict. If its RNA-Seq data and you want to find variants, use STAR with GATK.

   Since you are new I would encourage you to read more papers of exome, whole-genome and rna-seq basic wet lab prep and analytical workflow papers first and then rephrase your question and come back with places you get stuck.

[Medhat]

As said it is too much questions and not easy just to answer, you need to clarify each step, and each step has its own questions and answers: But as a start I would like you to have a look at BcBio

Answer 1

[Rahul Sharma]

I am also doing SNP analyses, I used following commands which could be of your interest, please adjust the input parameters accordingly:

In the following commands I am comparing two samples, prep2 and prep3, in this example I already have mapped .bam files. In case you have a single sample or file, you may input the single file and check parameters accordingly.

nohup samtools mpileup -t DP -uv -Q 15 -f /media/Storage/Analysis/mm9/genome.fa /media/Storage/Data/bam/prep2.bam /media/Storage/Data/bam/prep3.bam -o prep2-3_mpileup.vcf &

bcftools call -mv prep2-3_mpileup.vcf > Only_variations.vcf &
bcftools filter -s LowQual -e '%QUAL<20 || DP<30' Only_variations.vcf > Qualt20DP30_flt.vcf
grep -P "\tPASS\t" Qualt20DP30_flt.vcf > Qualt20DP30_flt.vcf.passed

After these filtering steps, you might be interested in figuring out which one of those SNPs are homozygous and heterozygous. This analysis can be done by grep out the 1/1 or 0/1 pattern in the last column of your vcf file. Please check the manual of VCFv4.2 for the description.

If you have any further questions, let me know.

Cheers, Rahul

Answer 2

[AB]

You can use VarScan. It can identify snp's and indels in multiple samples.

http://varscan.sourceforge.net/