GATK UnifiedGenotyper Stuck at "Preparing for traversal over 1 BAM files|"

Question

[sevvalakturk96]

By using GATK 3.2 IndelRealigner , one chromosome from a bam file was realigned. After that, it was sorted and SNP calling with UnifiedGenotyper was tried. However, without giving error it stops at the beginning and it says "Preparing for traversal over 1 BAM files|". Here the code for SNP calling:

/usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java -jar /usr/local/sw/GATK/GenomeAnalysisTK.jar -T UnifiedGenotyper -I xxx.bam -R yyy.fa -L ......1000G.bed --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES --alleles .......beagle.vcf.gz -o xxx.bam

The realigned bam file was validated via ValidateSamFile. The file is valid.

What could be the reason for that ? Any suggestions?

Answer 1

[Pierre Lindenbaum]

if 1000G.bed is big, gatk must find the section of the bam overlapping each region of the bed. And this is time consuming.

As a test, try to reduce your 1000G.bed to one line only and try again....