My objective is to identify the SNPs on resistance gene/haplotype.
I have resistance specific haplotype read and mapped bam file (ploidy = 1), susceptible haplotype read and mapped bam file (ploidy = 1) and other 9 susceptible varieties read and their mapped bam file (each variety with ploidy =4). I am using freebayes to identify the SNPs. I listed SNPs (vcf file) for resistance haplotype (ploidy setting =1) relative to reference genome, susceptible haplotype relative to reference genome (ploidy setting =1) and all other susceptible varieties (using multiple bam files) using same reference genome (ploidy setting =4). At the end I have 3 vcf file and doing calculation in excel to determine the resistance specific SNPs. The calculation now becomes more manual.
Do you have any idea on using freebayes to produce single vcf file or so that I will get SNPs (alternate allele ) in resistance haplotype relative to reference genome, susceptible haplotype and other susceptible varieties. Or can I call SNPs using multiple bam files of different ploidy level?
My general command is /bin/freebayes/bin/freebayes -f referencegenome.fasta --ploidy 1 --min-mapping-quality 10 --min-base-quality 10 --theta 0.01 --min-alternate-count 7 --min-alternate-fraction 0.2 --genotype-qualities --max-complex-gap 75 --pooled-continuous --haplotype-length 50 --use-reference-allele --min-supporting-mapping-qsum 10 --min-coverage 7 --use-best-n-alleles 6 --genotype-qualities --no-partial-observations mapped bam files | /vcflib/bin/vcffilter -f "QUAL > 40" > variant_output.vcf
Do you think, this command is okey? When calling SNPs using multiple bam file what extra setting I should add? I am very beginner in this field and any help is highly acknowledged. Thank you