Hi, I am working on variant calling with a fungal genome. When I am trying to reorder my .bam file (sorted) using picard ReorderSam (picard v2.9.0) to be used further in GATK realignment & BQSR, it throws this error:
Exception in thread "main" picard.PicardException: Discordant contig lengths: read scaffold1 LN=4751343, ref scaffold1 LN=4340956
Command I used,
java -jar /path/to/picard.jar ReorderSam I=myfile.bam O=reordered.bam R=myreference.fa
I checked my reference.fa file and found that the length of scaffold1 mention was incorrect (4751343), so I corrected it (LN=4340956) and created the .dict file again. But, I am still getting the same error.
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written
by
mirza
1 answer
Use option ALLOW_CONTIG_LENGTH_DISCORDANCE=true
If true, then permits mapping from a read contig to a new reference contig with the same name but a different length. Highly dangerous, only use if you know what you are doing
it's dangerous because it's highly probable that the reference associated to the BAM is different from the fasta reference .
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you're using the wrong reference file. You must use the very same reference file that was used to map the reads.
I am using the same reference file that I used for mapping.
show me
and
any command other than
cat myreference.fato view the reference coz' the reference has 2600 scaffolds! and I can see only the last few in my terminal. Anyhow, I am sure this is the same file.