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How to use the -L value in HaplotypeCaller?
I have exome seq made by using Agilent SureSelect v4 kit. I have downloaded the regions in BED files and transformed into this this format:
chr1:762097-762270 chr1:861281-861490 chr1:865591-865791 chr1:866325-866498 chr1:871059-871244 chr1:874364-874774
I am tring to provide the BEM file to the HaplotypeCaller:
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R human_g1k_v37.fasta -I result_sort_MarDup_AddRG_Indels_recal.bam -I exomes_from_1000G.list -o VCF_18_06_14 -stand_call_conf 30 -stand_emit_conf 10 -minPruning 3 -L regions.bed -nct 32
but I am getting empty VCF file
INFO 13:53:34,089 HaplotypeCaller - Ran local assembly on 0 active regions INFO 13:53:34,102 ProgressMeter - done 0.00e+00 0.0 s 38.1 h 0.0% 0.0 s 0.0 s INFO 13:53:34,102 ProgressMeter - Total runtime 0.14 secs, 0.00 min, 0.00 hours
If I am not using the -L function I am getting very large VCF file.
Should I provide diffrent format? How can I solve it?