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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.