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CollectReadCounts issue with preprocessedintervals file


With the release of the tutorial for gCNV calling, I tried running it again but encountered this error for CollectReadCounts:

htsjdk.tribble.TribbleException$MalformedFeatureFile: Error parsing line at byte position: LineIteratorImpl(SynchronousLineReader), for input source: TSO_exons_noflank_sorted.corrected.preprocessed.bed

The TSO_exons_noflank_sorted.corrected.preprocessed.bed was processed using this command line:

gatk PreprocessIntervals \
-R /mnt/storage/refs/human_1kg/human_g1k_v37.fasta \
-L TSO_exons_noflank_sorted.corrected.bed \
--bin-length 0 \
-O TSO_exons_noflank_sorted.corrected.preprocessed.bed

and the content of TSO_exons_noflank_sorted.corrected.bed looks like this:

1 955552 955753 AGRN
1 957580 957842 AGRN
1 970656 970704 AGRN
1 976044 976260 AGRN
1 976552 976777 AGRN
1 976857 977082 AGRN
1 977335 977542 AGRN
1 978618 978837 AGRN
1 978917 979112 AGRN
1 979202 979403 AGRN

So I'm not sure where the problem comes from since I've ran CollectReadCounts with the TSO_exons_noflank_sorted.corrected.bed file without processing with success.


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