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illustration about Resource Bundle

boymin2020boymin2020 New YorkMember
edited November 2016 in Ask the GATK team

Hi, I encountered a problem when using PrintReads function in the stage of BQSR.
The below is my command:

java -Xmx4G -jar $jar -T PrintReads -R $ref -I $bamFil -BQSR $table -o $out

Here the $ref is "human_g1k_v37.fasta" which was downloaded from the ./2.8/b37 folder of GATK Resource Bundle. Then an error came out.

ERROR MESSAGE: BUG: requested unknown contig=NC_007605 index=-1

I checked the bam file, it has a Reference sequence name: @SQ SN:NC_007605 LN:171823
But in the human_g1k_v37.fasta file, this no same record. It seems bam file has more sequence names than reference fasta file.
Then I used "human_g1k_v37_decoy.fasta" instead of the "human_g1k_v37.fasta", the script works.
I tried to find out the difference between the two files but failed.
Is there somebody can give me the detailed illustration about files in the Resource Bundle ???

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