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Hi, I'm using GATK latest version to analyze paired end exome sequencing data. I'd like to see the SNP, Indel and also SVs. I have followed the workflow of GATK, from the duplicates marking to the reads reducing step. Everything goes fine, until I start to use the HaplogypeCaller walker for the variant calling. Command line I used:
java -jar $GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R human_g1k_v37.fa -I sample_reduced.bam -o sample_variant.vcf
At the beginning, it worked well, then I got the error message of "Reads are too small for use in assembly." And I also tried the UnifiedGenotyper walker, command line：
java -jar $GATK/GenomeAnalysisTK.jar -T UnifiedGenotyper -R human_g1k_v37.fa -I sample_reduced.bam -glm BOTH -o sample_variant.vcf
I got an error message of "Read bases and read insertion quals aren't the same, size 46 vs. 49". I have googled the error message, but no related result. Does anyone met with the same problem? Eager to know how to solve this. Thanks!