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I get the following error when trying to read in a VCF file:
Error in .Call2("new_XStringSet_from_CHARACTER", ans_class, ans_elementType, :
key 42 (char '*') not in lookup table
The problematic entry is:
3 37067095 . ATATATTTTTT * 11571.2 PASS AC=1;AC_Orig=7;AF=0.5;AF_Orig=0.438;AN=2;AN_Orig=16;BaseQRankSum=-1.019;DP=2420;ExcessHet=3.01;FS=7.334;MQ=60;MQRankSum=0.356;QD=8.69;ReadPosRankSum=2.07;SOR=1.365 GT:AD:GQ:PL:SAC 0/1:121,56:99:1570,0,4899:86,35,0,0,47,9
The * character was introduced in VCF 4.2 to indicate that the allele is missing due to an upstream deletion.
Regards,
Christian
Hi,
I am using VariantAnnotation 1.16.1, but I get the same error:
Error in .Call2("new_XStringSet_from_CHARACTER", ans_class, ans_elementType, :
key 42 (char '*') not in lookup table
Do you have an idea about why it is not working, when I am using this version?
Josephine
Support for '*" is available in >= 1.16.0 so I'm not sure why this isn't working for you. Please show the output of sessionInfo() in the R session where you get the error.
If you can send me the file (valerie.obenchain@roswellpark.org) I can take a look.
Valerie
Thanks for sending the file. This was a bug and is now fixed in devel (1.17.6) and release ( 1.16.3). Both should be available via biocLite() tomorrow by noon PST or svn immediately.
Valerie