- Ann Arbor
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- Ann Arbor
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- Christopher Gillies
I fixed the issue by reindexing the known vcfs tabix -f -pvcf /home/cgillies/sequencing_reference_files/Mills_and_1000G_gold_standard.indels.hg19.sites.relabel.vcf.gztabix -f -pvcf /home/cgillies/sequencing_reference_files/1000G_phase1.indels.hg19.…
@Sheila Thanks for your help. I decided to use the UnifiedGenotyper for my use case. There are many false positives, but I have found that training an SVM to predict positive and negative sites removes the majority of the false sites. So I think my…
@Sheila Hi, Yes, one sample has the variant. It looks like changing the kmerSize parameter seems to fix the problem. Will this affect the sensitivity of calling other variants? Thanks, Chris
@Dalia Thanks for the information. I used the -dt NONE parameter to turn off downsampling for the UnifiedGenotyper. Yes, I agree that the allele balance heterozygous metric is very informative.
@Sheila I have put an archive named cgillies_HaplotypeCallerNotCallingSangerConfirmedVariant.zip with a snippet of problematic bam file. Please see commands.txt in the archive. Thank you for your help! @Dalia Thanks for posting this. Do you have …
@Sheila Thanks for your help Sheila! (Quote) Yes, you are correct those reads are duplicates. The data comes from a two-stage amplification. The first amplification happens in the Fluidigm system and the second amplification is on the standard PCR…
@Sheila Do you have any other suggestions for fixing this? I have found six examples across my cohort of 473 patients where we have a variant confirmed by Sanger sequencing, but HaplotypeCaller did not call the variant at the site. They all appear …
@Sheila Thank you for your response. Yes, the image I posted was the original bam. I generated a bamout with the following command and posted it: $JAVA -Xmx2048m -jar $GATK -T HaplotypeCaller -R $REF -I $BAM --dbsnp $DBSNP --emitRefConfidence GVC…
@Sheila Thank you! Your suggestion worked!
@Sheila Hi, I created an archive with the files I was using, and a file called commands.txt that lists all the commands. But the main commands are: $JAVA -Xmx2048m -jar $GATK -T HaplotypeCaller -R $REF -I $BAM --dbsnp $DBSNP --emitRefConfidence …
@Sheila Thanks. I was using GATK 3.4-0, which I think is the latest, so I must not be experiencing the same problem?
Has this bug been addressed yet? I think I am having a similar issue. GenotypeGVCFs is calling some sites as heterozygous when I can't see any evidence in the bam file. This is on a targeted sequencing project, I followed the best practices workflow…