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Poor SNP calling results
Hello, I'm new to the world of bioinformatics so apologies if this is not as detailed as some of the other questions!
I have performed the joint genotype haplotype caller on PCR free illumina sequencing of bacterial cells against a reference I produced by Pac-Bio. I've performed BWA mem, removing duplicates, indel realignment as described in your best practices. I cant do Base Recalibration due to lack of data. The BAM files produced at these stages look normal. I also created log files at each stage and these say that it ran successfully. However when I run Haplotype caller very few SNPS and Indels are identified in the g.vcf (4/5) and the bamout file visually looks empty (although it is ~170K in size).
I'm running GATK version 3.3. The code I'm using is:
Java -jar gatk.jar -R reference.fasta -T HaplotypeCaller -I preprocessed_reads.bam --pcr_indel_model --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -o sample1.g.vcf -bamout bamout.bam
Any help anyone could give me would be amazing as I'm really stuck!