Comments (4)
Hi, I found vardict-java will have the same bug. I edited the pipeline myself via this thread.
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Hi @lindenb,
No need to apologize! Thank you for reporting this and tracking down the source of the problem!
I think this issue originates with varscan's mpileup2cns
outputting REF alleles from the reference genome that GATK cannot handle. Based on this, it looks like the creators of VarScan have already identified this issue and are working on incorporating it into a new release of their software. There is also a Github issue for it here.
In the meantime, since there should be no call at these sites, one potential solution is to just discard records where this occurs. The VarCA pipeline will detect the absence of a variant at discarded sites and automatically label these sites as "no call", as they should be.
Here's a patch for the callers/varscan
script. I just deleted the last line and replaced it with an awk
command that should remove the problematic records.
--- a/callers/varscan
+++ b/callers/varscan
@@ -13,4 +13,4 @@ output_dir="$4"
samtools mpileup -l "$peaks" -f "$genome" -B "$bam" | \
varscan mpileup2cns --p-value 1 --strand-filter 0 --output-vcf > "$output_dir/varscan.vcf" && \
-bgzip -f "$output_dir/varscan.vcf" && tabix -p vcf -f "$output_dir/varscan.vcf.gz"
+awk -F $"\t" -v 'OFS=\t' '/^#/ || $4 !~ /^(R|Y|M|W|S|K|V|H|D|B|N)$/' "$output_dir/varscan.vcf" | \
+bgzip > "$output_dir/varscan.vcf.gz" && tabix -p vcf -f "$output_dir/varscan.vcf.gz"
If you have a chance, can you try this out and let me know if it resolves the problem?
from varca.
I've created pull request #26 for this patch. I can merge it into master and publish a new release once we are sure that it fixes the problem.
In the meantime, if anybody else runs into this issue, feel free to clone the patch/varscan-iupac
branch instead of master
. Please also leave a comment if this solves your problem!
from varca.
Personal correspondence with another VarCA user who ran into the same problem has indicated that the patch successfully resolves this issue. So I'll be merging this into master soon.
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