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How can I exclude snp sites with ALT asterisk by SelectVariants ?
I am using the latest GATK 3.6 to analysis my human WGS data.
For snp analysis, when I ran VariantRecalibrator , it reported error as following:
1 788419 . A * 854.77 PASS DP=33 GT 0/1
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '*'
I found that my raw.snp.vcf.gz had these sites :
chr1 64764 . C T
chr1 64976 . C T
chr1 66161 . T *
chr1 66164 . A *
chr1 66165 . T *
chr1 66166 . A *
chr1 66239 . A *
chr1 66240 . T *
chr1 66241 . T *
chr1 66242 . A *
I add parameter --selectTypeToExclude SYMBOLIC in SelectVariants but they were still in my snp.vcf.gz.
I don't know how to skip these sites and run VariantRecalibrator smoothly.
Thank you very much...