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Picard liftover from build 38 to 37 fails on alternate contigs
I am trying to lift a VCF from build 38 to build 37 using Picard liftover.
I'm using this chain file:
I get this error:
ERROR 2017-11-08 22:32:01 LiftoverVcf Encountered a contig, chr9_gl000199_random that is not part of the target reference.
I am deleting these problematic contigs from the chain file (using
curl -s http://hgdownload.cse.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz | gunzip -c | sed '/random/,/^$/d' hg38ToHg19.over.chain > hg38ToHg19.over.modified.chain). Is that an OK approach?
However, now I get this error:
INFO 2017-11-08 23:35:39 LiftOver Interval chr18:15781697-15781698 failed to match chain 1430656 because intersection length 1 < minMatchSize 2.0 (0.5 < 1.0)
I'm getting the same error as described in this thread while trying to lift over in the opposite direction.
Is it possible to achieve what I want? Thanks Sheila, Geraldine and "shlee".