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Picard LiftoverVcf b37tohg19 - gatk GetPileupSummaries works for b37, error for liftovered hg19

Adam_U0Adam_U0 Member
edited September 2018 in Ask the GATK team


I'd like to perform gatk GetPileupSummaries for my .bam file. However I'm using hg19 as reference through all steps of analysis. Hence I decided to make a LiftOverVcf to get .vcf based on hg19 so:

gatk GetPileupSummaries \
-I my_tumor.bam \
-V small_exac_common_3_hg19.vcf \
-O my_tumor.table

To get small_exac_common_3_hg19.vcf I run:

java -Xmx6g -jar picard.jar LiftoverVcf \
     I=small_exac_common_3_b37.vcf \
     O=small_exac_common_3_hg19.vcf \
     CHAIN=b37tohg19.chain \
     REJECT=rejected_variants.vcf \

I have to mention that I removed 'chr' from chain file, because it cased errors like this https://gatkforums.broadinstitute.org/gatk/discussion/11218/picard-liftovervcf-error-when-attempting-to-liftover-to-build-38

Function went fine that I recieved small_exac_common_3_hg19.vcf.

When I run:

   gatk GetPileupSummaries \
    -I my_tumor.bam \
    -V small_exac_common_3_hg19.vcf \
    -O my_tumor.table

Then error occured:

htsjdk.tribble.TribbleException$MalformedFeatureFile: Error parsing line at byte position: LineIteratorImpl(SynchronousLineReader)

However when I run whole function with b37 - success.

       gatk GetPileupSummaries \
        -I my_tumor.bam \
        -V small_exac_common_3_b37.vcf \
        -O my_tumor.table

In addition to this, I compared both .vcf's - b37 and hg19. They look exactly the same. The only difference is in the dec symbols in numbers; b37 has dots in QUAL column where hg19 has commas.

So my questions are: how to avoid this problem?
Shall I ignore it and use b37 for gatk GetPileupSummaries function?
Is it ok, that both small_exac_common files (b37 and hg19 after lift over) are the same?
As far as I know those references are pretty simillar, there are minor changes; so maybe I didn't catch them?

Many thanks,

Post edited by Adam_U0 on

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