vcf files in gatk not showing data lines

Question

[jamessemaj712]

Hi,

I tried using Gatk tool to find variants in a chromosome 21 of human genome. I used HaplotypeCaller tool for finding the variants using the following command:

java -jar GenomeAnalysisTK.jar -R chr21/chr21.fa -T HaplotypeCaller -I chr21/alignments/human38chr21.sorted.bam -o chr21/variants/answerold.raw.snps.indels.vcf

as given on following url: https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php

I got a vcf file but it contains only the header part and there is not data lines in it.What is wrong?

[Vivek]

Can you post the stack trace you get when you run this command?

[jamessemaj712]

INFO  10:43:04,724 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  10:43:04,734 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56 
INFO  10:43:04,734 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  10:43:04,734 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  10:43:04,747 HelpFormatter - Program Args: -R chr21/chr21.fa -T HaplotypeCaller -I chr21/alignments/human38chr21new.sorted.bam -o chr21/humanoutput.raw.snps.indels.vcf 
INFO  10:43:04,763 HelpFormatter - Executing as aditya@aditya-VirtualBox on Linux 3.19.0-56-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-internal-b14. 
INFO  10:43:04,775 HelpFormatter - Date/Time: 2016/04/06 10:43:04 
INFO  10:43:04,775 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  10:43:04,776 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  10:43:05,009 GenomeAnalysisEngine - Strictness is SILENT 
INFO  10:43:05,377 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500 
INFO  10:43:05,410 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  10:43:05,571 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.16 
INFO  10:43:05,647 HCMappingQualityFilter - Filtering out reads with MAPQ < 20 
INFO  10:43:06,050 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO  10:43:06,448 GenomeAnalysisEngine - Done preparing for traversal 
INFO  10:43:06,451 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  10:43:06,458 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining 
INFO  10:43:06,458 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime 
INFO  10:43:06,469 HaplotypeCaller - Disabling physical phasing, which is supported only for reference-model confidence output 
INFO  10:43:06,618 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values. 
WARN  10:43:06,621 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples. 
INFO  10:43:06,622 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values. 
INFO  10:43:06,879 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units 
Using AVX accelerated implementation of PairHMM
INFO  10:43:11,839 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file 
INFO  10:43:11,842 VectorLoglessPairHMM - Using vectorized implementation of PairHMM 
INFO  10:43:36,488 ProgressMeter -  chr21:10690236              0.0    30.0 s           49.7 w       22.9%     2.2 m     101.0 s 
INFO  10:44:06,490 ProgressMeter -  chr21:17044140              0.0    60.0 s           99.3 w       36.5%     2.7 m     104.0 s 
INFO  10:44:36,494 ProgressMeter -  chr21:22543743              0.0    90.0 s          148.9 w       48.3%     3.1 m      96.0 s 
INFO  10:45:06,496 ProgressMeter -  chr21:27653512              0.0   120.0 s          198.5 w       59.2%     3.4 m      82.0 s 
INFO  10:45:36,497 ProgressMeter -  chr21:33975834              0.0     2.5 m          248.1 w       72.7%     3.4 m      56.0 s 
INFO  10:46:06,499 ProgressMeter -  chr21:40228258              0.0     3.0 m          297.7 w       86.1%     3.5 m      29.0 s 
INFO  10:46:36,130 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.06849923200000001 
INFO  10:46:36,130 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.20202936 
INFO  10:46:36,131 HaplotypeCaller - Ran local assembly on 0 active regions 
INFO  10:46:36,133 ProgressMeter -            done      4.6709983E7     3.5 m            4.0 s      100.0%     3.5 m       0.0 s 

[jamessemaj712]

INFO  10:46:36,135 ProgressMeter - Total runtime 209.68 secs, 3.49 min, 0.06 hours 
INFO  10:46:36,135 MicroScheduler - 169827 reads were filtered out during the traversal out of approximately 962428 total reads (17.65%) 
INFO  10:46:36,135 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter 
INFO  10:46:36,136 MicroScheduler -   -> 0 reads (0.00% of total) failing DuplicateReadFilter 
INFO  10:46:36,137 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter 
INFO  10:46:36,137 MicroScheduler -   -> 169827 reads (17.65% of total) failing HCMappingQualityFilter 
INFO  10:46:36,138 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter 
INFO  10:46:36,138 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter 
INFO  10:46:36,139 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter 
INFO  10:46:36,150 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter 
INFO  10:46:37,534 GATKRunReport - Uploaded run statistics report to AWS S3 

[jamessemaj712]

I have added the stack trace in 2 replies due to limit placed on the number of characters in the reply text area.

[Jessica L]

I've also had issues with some of the GATK tools outputting what were basically empty vcf files. I found that running the base recalibrator before I ran haplotype caller changed my outputs significantly. I wonder if you're not running into something similar.

[jamessemaj712]

where do I get to known sites parameter.I can't find it.

[Zaag]

approximately 962.428 total reads

So you have less than 1 million reads for all of chr21?

[H.Hasani]

Have you tried to use GATK forum? This seems GATK specific.

[fernardo]

what is the size of your bam file?

Also try to see inside bam file with:

samtools tview chr21/chr21.fa chr21/alignments/human38chr21.sorted.bam

Then give us a feedback.

[reza.jabal]

Are u running this locally or on the cluster?