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Help me check my picard style intervals list file.

Hello, I used BedToIntervalList to convert bed file to interval list file. My intervals list file:

@SQ SN:chr18_gl000207_random LN:4262 M5:f3814841f1939d3ca19072d9e89f3fd7 UR:file:/mnt/hg19/bigZips/hg19.fa
chr1 30331 30540 + .
chr1 35052 35529 + .
chr1 35624 35833 + .
chr1 69040 70059 + .
chr1 367619 368638 + .
chr1 567645 567854 + .
chr1 621056 622075 + .
chr1 721375 721944 + .
This is invalid format? Because I passed this interval list file to `-L` of command `SelectVariants` and got error. Error:


A USER ERROR has occurred: File /share/Data01/pengguoyu/Project/AutoDNA/Resources/WES/BGI_ex_region_hg19.interval_list is malformed: Interval file could not be parsed in any supported format. caused by Couldn't read file file:///share/Data01/pengguoyu/Project/AutoDNA/Resources/WES/BGI_ex_region_hg19.interval_list. Error was: file:///share/Data01/pengguoyu/Project/AutoDNA/Resources/WES/BGI_ex_region_hg19.interval_list has an invalid interval : chr1:30331-30540 + .

This is because the target field is "." in my file?

Best Answer


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