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Alignments were done with bwa, paired end, converted to .bam and sorted with samtools.
The following command works as expected. It makes a vcf file that is 10 kb, which is right.
The following command makes a vcf file that is 57.5 kb
What happens is that at base 2256558, something gets off by a base, so that it calls another 300,000 SNPs, because it's all out of sync. This doesn't happen in the first command, even though it covered almost exactly the same ground. The fasta looks fine. Has anyone else ever observed this?
The following command works as expected. It makes a vcf file that is 10 kb, which is right.
java -jar ../../../../GATK/1.1.23/GenomeAnalysisTK.jar -T UnifiedGenotyper -R genome3.fasta -I sort_filtered.bam -o GATK/regular.vcf -L Staphylococcus:164665-2689091 -dcov 100
java -jar ../../../../GATK/1.1.23/GenomeAnalysisTK.jar -T UnifiedGenotyper -R genome3.fasta -I sort_filtered.bam -o GATK/regular.vcf -L Staphylococcus:164663-2689091 -dcov 100