Missing BED files for exome fastqs

genome-in-a-bottle / giab_data_indexes

This repository contains data indexes from NIST's Genome in a Bottle project.

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Missing BED files for exome fastqs #2

Closed vladimirkovacevic closed 4 years ago

vladimirkovacevic commented 7 years ago

Do you have available capture BED files for NA12878_Illumina_HiSeq_Exome_Garvan_trimmed_fastq_09252015?

chunlinxiao commented 7 years ago

is this what you are looking ofr?

ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/nexterarapidcapture_expandedexome_targetedregions.bed.gz

uros-sb commented 4 years ago

Is this BED for assembly 37 or 38?

chunlinxiao commented 4 years ago

the README file does not mention whether this data is b37 or b38 based; but the vcf file project.NIST.hc.snps.indels.vcf clearly mentioned hg19/grch37 in the header as below:

contig=

uros-sb commented 4 years ago

Yeah great, thank you for answering, even though this issue was 3 years old :)