If I am getting
ERROR: Bit::Vector::Interval_Fill(): maximum index out of range at /usr/local/share/perl/5.14.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 232, <gen4> line 301403.
Is there a way of telling which file is providing the "out of range" value? The reference, the MAF or the ROI file? Our BAMs were aligned using the g1k version37 reference. Our SNP calls were also done using this reference. I am now trying to use the GRCh37.73 reference, which from my reading, seemded to be similar except for the mitochondrial naming (MT calls were removed from the MAF anyhow) and the unlocalized, unplaced and alternate loci. If the BAMs and SNPs were processed with one reference, is there no way to change things downstream? (I think I know the answer, but I'm hoping...)
Thank you, DD
Line 232 in CalcBmr.pm fails on line 301403 of your ROI file. Can you post a sample of your ROI file, or take a look at line 301403?
Lines 301402 - 301407
In the index, the relevant line is
So the extent of the ROI in questions is on too large; perhaps it should be 180455 (or, since the indexed region is 180455 it should be 1 - 180456 ?) Making that change fixes the problem! I guess adding a flanking base pair to that ROI make it too big for the index.
Related question, if I get an error such as:
Does <GEN6> refer to a certain input file? There were 5 in that case (
genome music bmr calc-bmr --bam-list=/media/data/bamlist.csv --reference-sequence=/home/registry3/Documents/reference/human_g1k_v37.fasta --roi-file=/home/registry3/Documents/reference/human_g1k_v37_level1_gencode_ROI_for_music --output-dir=/media/data/music_output1/ --maf-file=/media/data/10patients.MAF
)