BWA alignment for multiple genotypes

[shis]

Hello expert members,
I would like to get your advice regarding BWA alignment options. I found in the bwa manual that it uses only two read files for paired-end and one read file for single-end data at a time. However, I have 3 genotypes (each has two fastq files) to identify and compare SNPs among them. According to the BWA guideline, I used two (read1.fastq and read2.fastq) files of one genotype at a time to make alignment against the reference genome using the following command line:

bwa mem ref.fasta BH_1.fastq_filtered BH_2.fastq_filtered > aln-BH.sam
bwa mem ref.fasta Cyp_1.fastq_filtered Cyp_2.fastq_filtered > aln-Cyp.sam
bwa mem ref.fasta SR_1.fastq_filtered SR_2.fastq_filtered > aln-SR.sam

Now I have 3 *.sam files for the 3 genotypes for SNPs variant calling. My question - is it possible to use all 6 fastq files from 3 genotypes in the single command to get a single *.sam file like below:

bwa mem ref.fasta BH_1.fastq_filtered BH_2.fastq_filtered Cyp_1.fastq_filtered Cyp_2.fastq_filtered SR_1.fastq_filtered SR_1.fastq_filtered > aln-bwa.sam

Thank you so much for taking your valuable time and I would appreciate your advice.

Thanks
Shofi

[shis]

How to compare vcf file containing snps between two cultivars

Hi all,
I have three vcf files containing SNPs of three different cultivars. The SNPs were called using GATK's UnifiedGenotyper program. After stringent filtering with GATK's hard filters, I have approx. approx. 3.5 millions SNPs in the three cultivars. Now I would like to compare between two cultivars based on the vcf files to identify common and specific SNPs in vcf1/vcf2, vcf1/vcf3 and vcf2/vcf3, and also like to generate venn diagram.

Can anyone suggest me - which tool I can use to identify common and specific SNPs between two cultivars? I do appreciate your help.

[Brian Bushnell]

Coincidentally, I just released a program for this purpose, in the BBMap package. You can use it like this:

comparevcf.sh in=sample1.vcf,sample2.vcf out=difference.vcf subtract

It supports union, intersection, and subtraction. Note that subtraction is order-dependent while the other operations are not.