HaplotypeCaller prints empty VCF file

sarthaksarthak netherlandsMember

I am trying to do variant-only calling for DNA sequence using the following command:
java -Xmx5120m -jar GenomeAnalysisTK.jar -T HaplotypeCaller -nct 4 -R ucsc.hg19.fasta -I region0-3.bam -o region0.vcf -stand_call_conf 30 -stand_emit_conf 10 -L bed0.bed --no_cmdline_in_header --disable_auto_index_creation_and_locking_when_reading_rods

It gave the following output:

INFO 09:39:42,782 HaplotypeCaller - Ran local assembly on 0 active regions
INFO 09:39:42,806 ProgressMeter - done 1.76e+06 2.0 s 1.0 s 100.0% 2.0 s 0.0 s
INFO 09:39:42,808 ProgressMeter - Total runtime 2.01 secs, 0.03 min, 0.00 hours
INFO 09:39:42,808 MicroScheduler - 488 reads were filtered out during the traversal out of approximately 507 total reads (96.25%)
INFO 09:39:42,809 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
INFO 09:39:42,810 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 09:39:42,811 MicroScheduler - -> 488 reads (96.25% of total) failing HCMappingQualityFilter
INFO 09:39:42,811 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 09:39:42,812 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
INFO 09:39:42,813 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
INFO 09:39:42,813 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter

The vcf file appears to be empty:

reference=file:///data/spark/ref/ucsc.hg19.fasta

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1

Could someone please tell what can be the possible cause of this?

Answers

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