Hi,
I am doing variant calling using as reference hg19. After Gatk Mutect with PON Mutect2-WGS-panel-b37.vcf transformed into Mutect2-WGS-panel-b37-hg19.vcf and germline af-only-gnomad.raw.sites.vcf to af-only-gnomad.hg19.raw.sites.vcf (with Picard LiftOver).
After doing Mutect2 next step is GATK GetPileUpSummaries, that has this usage from GATK website:
gatk GetPileupSummaries \
-I tumor.bam \
-V common_biallelic.vcf.gz \
-L common_biallelic.vcf.gz \
-O pileups.table
And the tutorial https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/#tumor-only-variant-calling-workflow :
GetPileupSummaries
-I Tumor_Sample_Alignment.bam \
-O <job_identifier>.targeted_sequencing.table \
-V af-only-gnomad-common-biallelic.grch38.main.vcf.gz \ # Germline reference from gnomad
-L intervals.bed \ ## Only chr1-22 + XYM
-R GRCh38.d1.vd1.fa
I want to ask what should the -V and -L be? And where to find these files? Can af-only-gnomad.hg19.raw.sites.vcf be the -V argument given that this file seems not to be biallelic and where can I find the intervals.bed file for hg19 or b37 to be converted into hg19?
