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window size in haplotypecaller's output bam

mrooneymrooney Cambridge, MAMember


I am using HaplotypeCaller to re-align reads according to a set of pre-existing somatic variant calls. So far, this seems to work well; however, when I review the output bam in IGV, I notice that HC only provides 20nt of context upstream and downstream of each variant site. I am wondering how to boost this to a larger window size, say 100, so I can see more context. I saw a couple of other threads discussing a "-L" argument, but I could not quite figure it out. I have pasted my current command below.

Thanks in advance,

java -Xmx18000M -jar /opt/GenomeAnalysisTK_3.5-0-g36282e4.jar
--analysis_type HaplotypeCaller
--out hc_out.vcf
--bamout hc_out.bam
--standard_min_confidence_threshold_for_emitting 20
--standard_min_confidence_threshold_for_calling 20
--reference_sequence HG19.gencode.fasta
--input_file hc_in.bam
--intervals hc_in.vcf
--interval_padding 500
--genotyping_mode GENOTYPE_GIVEN_ALLELES
--gatk_key gatk.key
--dbsnp germline.vcf
--alleles hc_in.vcf

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