The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
GATK Haplotypecaller missing variants
I am trying to use GATK HP ( v3.5 ) to call SNPs in amplicon seq data of a small genome of around 600bp. As shown in the attachment, the variants are not called between location 50 and 60, despite high coverage across many samples. ( There are total 96 samples ).
The base qualities are above 30 and mapping quality is also 60 ( bwa mem ). I also did not remove duplicates ( not marked as well ) as its amplicon seq data.
The command I used was ( multisample SNP calling ) :
java -Xmx50g -jar GenomeAnalysisTK.jar -nct 2 -R<in.fasta> -T HaplotypeCaller -I merged_samples.bam -o gatk_out_raw_snps_indels.vcf --min_base_quality_score 30
Its the same case even with base quality 20.
Thanks in advance.