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Should I provide the exome target list (-L argu) even while calling gVCF file using Haplotypecaller?
Recently we performed exome sequencing using Nextera Illumina platform for three samples (Father, Mother and Son). I downloaded the exome interval list from Illumina's website.
1) Trimmed the raw reads
2) Aligned the trimmed reads against the human reference hg19 as recommended for exome-sequencing
3) Then sorted, deduped, recalibrated the bam file.
4) Then performed variant calling in two steps process for all three samples individually
4.1) Used the GATK Haplotype Caller tool in GVCF mode
Command: java -Xmx16g -jar GenomeAnalysisTK.jar - T Haplotypecaller -R /GATK_bundle/hg19.fa -I sample1.sorted.dedup.recal.bam --emitRefConfidence GVCF --dbsnp /GATK_bundle/dbsnp.138.hg19.vcf -o sample1.raw.g.vcf
4.2) Used GenotypeGVCFs (Joint SNP calling) for all three samples together
Command: java -Xmx16g -jar GenomeAnalysisTK.jar - T GenotypeGVCFs -R /GATK_bundle/hg19.fa --variant sample1.raw.g.vcf --variant sample2.raw.g.vcf --variant sample3.raw.g.vcf --dbsnp /GATK_bundle/dbsnp.138.hg19.vcf -o sample1.2.3.trio.raw.vcf
In the above command, I didn't use the Illumina's exome interval list used for targeting the exomes in sequencing process.
As per this link "https://software.broadinstitute.org/gatk/documentation/article.php?id=4669", under the example section of GATK command lines, for exome sequencing the article suggests us to provide the exome targets using -L argument.
I have following queries,as per the aforementioned article
1) Should I provide the exome target list (-L argument) only while calling regular VCF file using Haplotype caller?
2) Should I provide the exome target list (-L argument) even while calling gVCF file using Haplotype caller?