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I would appreciate your thoughts on the following pipeline:
I'm currently working on a number of WGS of non-human vertebrates. My approach for calling variants is to maximize the sensitivity of the calls by using two callers (GATK's UnifiedGenotyper + samtools' mpileup) per chromosome regardless of / ingnoring all filters. Next, I would like to merge (not intersect) the two vcf files (GATK+samtools) per each chromosome, then merge (not intersect) all the vcf files pertaining to all chromosomes in order to retrieve a final vcf dataset per individual:
For merging the GATK and samtools:
$ java -Xmx10g -jar GenomeAnalysisTK.jar -T CombineVariants -R ref.fasta --variant:GATK chr#.GATK.vcf --variant:samtools chr#.samtools.vcf -o chr#.GATK_samtools.union.vcf -genotypeMergeOptions PRIORITIZE -priority GATK,samtools --filteredrecordsmergetype KEEP_UNCONDITIONAL
For merging all chromosomes per individual:
$ java -Xmx10g -jar GenomeAnalysisTK.jar -T CombineVariants -R ref.fasta --variant:chr1 chr1.GATK_samtools.union.vcf --variant:chr2 chr2.GATK_samtools.union.vcf --variant:chr3 chr3.GATK_samtools.union.vcf -o Individual1.union.vcf -genotypeMergeOptions PRIORITIZE -priority chr1,chr2,chr3 --filteredrecordsmergetype KEEP_UNCONDITIONAL
Finally I would like to intersect between two individuals and keep only the variants that are common to both individuals:
Uniting / merging two individuals:
$ java -Xmx10g -jar GenomeAnalysisTK.jar -T CombineVariants -R ref.fasta --variant:individual1 Individual1.union.vcf --variant:Individual2 Individual2.union.vcf -o Individual1_2.union.vcf -genotypeMergeOptions PRIORITIZE -priority Indiviual1,Individual2 --filteredrecordsmergetype KEEP_UNCONDITIONAL
Intersecting the two indiviuals in order to keep only common variants:
$ java -Xmx10g -jar GenomeAnalysisTK.jar -T SelectVariants -R ref.fasta --variant Individual1_2.union.vcf -select 'set == "Intersection";' -o Intersected.vcf
Am I doing this right? I'm afraid I may be losing variants or something else along this pipeline. Remember that I want to keep only the common variants while ignoring the filters in order to increase sensitivity as much as possible.