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LiftoverVcf no output
I'm using LiftoverVcf to make a hg38 version of the gnomad file from the GATK resource bundle
The gnomad file is in b37 version, as there isn't a chain file for b37 -> hg38, I have to do b37 -> hg19, and then hg19 -> hg38 (even if I'm not very enthusiast to do so).
Anyway, I performed the first "conversion step" with the following command line:
java -Xmx8g -jar picard.jar LiftoverVcf I=~/af-only-gnomad.raw.sites.b37.vcf.gz O=~/af-only-gnomad.raw.sites_LIFTOVERhg19.vcf CHAIN=~/b37tohg19.chain REJECT=~/af-only-gnomad.raw.sites_LIFTrejected19.vcf R=~/hg19_M_rCRS.fasta
The result was an empty VCF file, I thought that something went wrong and looked at the "rejected" file, but it was empty as well...it only contained the Header (I don't even know if it is normal that the header is rejected)
the log on the terminal was this:
INFO 2017-12-06 13:20:39 LiftoverVcf Loading up the target reference genome. INFO 2017-12-06 13:20:45 LiftoverVcf Lifting variants over and sorting. INFO 2017-12-06 13:20:51 LiftoverVcf read 1.000.000 records. Elapsed time: 00:00:05s. Time for last 1.000.000: 5s. Last read position: 1:9.514.996 INFO 2017-12-06 13:20:55 LiftoverVcf read 2.000.000 records. Elapsed time: 00:00:09s. Time for last 1.000.000: 4s. Last read position: 1:19.801.042 [...] INFO 2017-12-06 13:37:29 LiftoverVcf read 267.000.000 records. Elapsed time: 00:16:44s. Time for last 1.000.000: 3s. Last read position: X:131.552.026 INFO 2017-12-06 13:37:33 LiftoverVcf read 268.000.000 records. Elapsed time: 00:16:48s. Time for last 1.000.000: 3s. Last read position: X:146.780.876 INFO 2017-12-06 13:37:36 LiftoverVcf Processed 268545311 variants. INFO 2017-12-06 13:37:36 LiftoverVcf 0 variants failed to liftover. INFO 2017-12-06 13:37:36 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. INFO 2017-12-06 13:37:36 LiftoverVcf 0,0000% of variants were not successfully lifted over and written to the output. INFO 2017-12-06 13:37:36 LiftoverVcf Writing out sorted records to final VCF. [Wed Dec 06 13:37:36 CET 2017] picard.vcf.LiftoverVcf done. Elapsed time: 16,96 minutes. Runtime.totalMemory()=7299137536 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" java.lang.NumberFormatException: For input string: "30,35" at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043) at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110) at java.lang.Double.parseDouble(Double.java:538) at java.lang.Double.valueOf(Double.java:502) at htsjdk.variant.vcf.AbstractVCFCodec.parseQual(AbstractVCFCodec.java:518) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:322) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:284) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:262) at htsjdk.variant.vcf.VCFRecordCodec.decode(VCFRecordCodec.java:53) at htsjdk.variant.vcf.VCFRecordCodec.decode(VCFRecordCodec.java:18) at htsjdk.samtools.util.SortingCollection$FileRecordIterator.advance(SortingCollection.java:497) at htsjdk.samtools.util.SortingCollection$FileRecordIterator.<init>(SortingCollection.java:469) at htsjdk.samtools.util.SortingCollection$MergingIterator.<init>(SortingCollection.java:407) at htsjdk.samtools.util.SortingCollection.iterator(SortingCollection.java:273) at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:329) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:268) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)
According to it, it seems that 0 variants failed to liftover, but they weren't printed in the output file.
I also don't actually know what the last lines of the log mean...I'm talking about "Exception in thread etc. etc. ..."