Hi everyone,
I'm trying to convert a bed file into interval list format. I'm not sure about which file I should choose as SD. I've tried using 'genome.dict' (genome.fa is the reference genome I've used to align) or the BAM file of the aligned reads; in both cases I get the following error:
Exception in thread "main" picard.PicardException: Sequence 'chr1_KI270763v1_alt' was not found in the sequence dictionary
How can I solve this issue?
Thanks in advance
•
written
by
Elisa •
1 answer
Sequence 'chr1_KI270763v1_alt' was not found in the sequence dictionary
your bed file contains a chromosome "chr1_KI270763v1_alt" that is not defined in the REFERENCE/DICT file.
if you're not interested with that contig, you can just remove it from your bed with grep -v
it depends of your downstream analysis. For example if you're using a bam and gatk, the internal dictionary should be the very same than the reference sequence.
Log in to answer this question.
-
bbmap read length from fastq
written by marco.barr •
-
Troubles with Pysim-sv simulator
written by Elisa •
-
Bed to Interval list for CollectHsMetrics picard
written by aroso491 •
-
How to prepare vcf for use with Picard?
written by optimistsso4co3 •
-
Issues with CollectAlignmentSummaryMetrics Picard tool
written by Elisa •
-
Issues with CollectAlignmentSummaryMetrics Picard tool
written by Elisa •
-
Picard CollectSequencingArtifactMetrics error
written by jrleary
-
Understanding Picards HsMetrics
written by finswimmer
-
MCScanX Error - Can't plot the graphs (Downstream analysis)
written by oliveira.bhn •
-
error using the F-seq tool
written by rsabrina93 •
