GATK UnifiedGenotyper doesn't output the variants in vcf files

Question

[GK1610]

Hi

I am trying to generate genotype likelihoods from a bam file using UnifiedGenotyper. I am following Pasaniuc Nature genetics 2012 Supplementary note 10 pipeline.

The input was

java -Xmx4g -jar gatk/3.6-0/src/GenomeAnalysisTK.jar -T UnifiedGenotyper    -R ucsc.hg19.fasta    -I my.bam    -o my.vcf.gz    -rf DuplicateRead    -gt_mode GENOTYPE_GIVEN_ALLELES    -out_mode EMIT_ALL_SITES

Thats how the last lines of command line output looks like:

INFO  06:59:27,491 ProgressMeter -  chrX:150773001   3.031782657E9     2.3 h       2.0 s       96.6%     2.4 h       4.8 m
INFO  06:59:57,492 ProgressMeter -   chrY:11394929   3.046429345E9     2.3 h       2.0 s       97.1%     2.4 h       4.1 m
INFO  07:00:37,493 ProgressMeter - chr6_dbb_hap3:3150129   3.109882985E9     2.3 h       2.0 s       99.1%     2.4 h      73.0 s
INFO  07:01:17,493 ProgressMeter - chr6_ssto_hap7:4256557   3.129719754E9     2.3 h       2.0 s       99.8%     2.3 h      20.0 s
DEBUG   2018-06-22 07:01:47 BlockCompressedOutputStream Using deflater: Deflater
INFO  07:01:47,209 ProgressMeter -            done   3.137161264E9     2.4 h       2.0 s      100.0%     2.4 h       0.0 s
INFO  07:01:47,209 ProgressMeter - Total runtime 8460.20 secs, 141.00 min, 2.35 hours
INFO  07:01:47,209 MicroScheduler - 4781074 reads were filtered out during the traversal out of approximately 1107673498 total reads (0.43%)
INFO  07:01:47,209 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
INFO  07:01:47,209 MicroScheduler -   -> 3520170 reads (0.32% of total) failing BadMateFilter
INFO  07:01:47,212 MicroScheduler -   -> 0 reads (0.00% of total) failing DuplicateReadFilter
INFO  07:01:47,212 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO  07:01:47,212 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO  07:01:47,214 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
INFO  07:01:47,215 MicroScheduler -   -> 309492 reads (0.03% of total) failing NotPrimaryAlignmentFilter
INFO  07:01:47,215 MicroScheduler -   -> 951412 reads (0.09% of total) failing UnmappedReadFilter

but my vcf file is empty. it has only headers. Can you help me with this?

Answer 1

[Pierre Lindenbaum]

-gt_mode GENOTYPE_GIVEN_ALLELES Specifies how to determine the alternate alleles to use for genotyping

--alleles / -alleles Set of alleles to use in genotyping When --genotyping_mode is set to GENOTYPE_GIVEN_ALLELES mode, the caller will genotype the samples using only the alleles provide in this callset. Note that this is not well tested in HaplotypeCaller

you didn't specify a value for --alleles . But I think you just don't want this -gt_mode