Tagged with #bacteria
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I have used GATK for human. Now i have a need to call variants from bacteria. In case of human, known variants is fed in Base quality recalibration step, however, i do not have any know variants for bacteria, can i simply skip the step of Base quality recalibration? I gave a try by skipping it, but i got exceptionally huge number of SNPs. Are there any strict requirements for bacteria variant call?

Comments (1)

I'm trying to call variants on metagenomic data using the UnifiedGenotyper. I know that the diploid genotype calls & likelihoods will not be valid since my data is not diploid, but I want to use the vcf output so sum up base frequencies at detected variant loci.

I mapped 100+ samples (each being ~2 Illumina GA2 lanes of data that after host filtering usually contain about 20-40 million reads per sample) against a database of 671 bacterial reference sequences (and each reference can be in multiple parts, so I probably have 10s of thousands of sequence records in my ref db, spanning the 671 reference genomes...around 2.2Gb in total size). I am then feeding the resulting 100+ bam files to the UnifiedGenotyper.

After some initial mistakes on my part (yes I have entered the future and am using GATK 2.2-5 now :) ) I've now started a run in proper fashion, but after a couple hours its dying with the message that the java application has run out of memory:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.2-5-g3bf5e3f):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: There was a failure because you did not provide enough memory to run this program. See the -Xmx JVM argument to adjust the maximum heap size provided to Java
ERROR ------------------------------------------------------------------------------------------

I had set -Xmx60g for that failed run, so now I'm wondering if its possible to estimate how much memory would be needed for this job I'm trying to run. Do you think a job of this size is even possible with the UG? Is it the number of references that is killing me here? Or the number of samples?

Comments (3)

Hi,

I am fairly new to GATK, but am trying to call SNPs in two bacterial strains against a single reference. In one strain the SNP is called, but not the other... looking at the alignment in IGV and also all sites (-out_mode EMIT_ALL_SITES) I can't understand why the SNP was not called in the second strain.

For the first strain, for which GATK calls the SNP NC_011770 9650 . C T 645.75 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-2.149;DP=43;Dels=0.05;FS=4.191;HRun=2;HaplotypeScore=5.6633;MQ=64.95;MQ0=0;MQRankSum=0.878;QD=15.02;ReadPosRankSum=2.270;SB=-255.73 GT:AD:DP:GQ:PL 1/1:2,39:41:46.50:679,46,0

For the second strain, for which GATK does NOT call the SNP: NC_011770 9650 . C T 942.90 PASS AC=2;AF=1.00;AN=2;DP=53;Dels=0.06;FS=0.000;HRun=2;HaplotypeScore=23.7546;MQ=53.63;MQ0=0;QD=17.79;SB=-393.80 GT:AD:DP:GQ:PL 1/1:0,47:50:99:976,105,0

UnifiedGenotyper was called with these options:

-stand_call_conf 30.0 -stand_emit_conf 10.0 -dcov 100 -out_mode EMIT_ALL_SITES

Does anyone know why GATK does not call a SNP in the second strain?

Thanks for any help

Adam