I encountered an error while using the SnpSift caseControl command to analyze a VCF file. The error message is:
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 10
at org.snpsift.SnpSiftCmdCaseControl.annotate(SnpSiftCmdCaseControl.java:76)
at org.snpsift.SnpSiftCmdCaseControl.run(SnpSiftCmdCaseControl.java:411)
at org.snpsift.SnpSiftCmdCaseControl.run(SnpSiftCmdCaseControl.java:388)
at org.snpsift.SnpSift.run(SnpSift.java:588)
at org.snpsift.SnpSift.main(SnpSift.java:76)
The command that triggered this error is:
SnpSift caseControl -name "group1" "--0--000-0+++0-0-0-0-0+--0-++-0--0---+--0+0+-0+--+0--++0--0-00-++00++0+---+--0000++0+-0-+-++-0++000-0+00-000++-++-0-0--+-----0-+----0----++0-----0-0-0-0----00---+00--+---0++-00++--00++--0+0---+0-" input.vcf
The input VCF file contains 204 columns (with the standard header columns+my 195 samples), and I have verified the file is correctly formatted with no missing or malformed lines. I have previously used snpsift with other commands (like filter o annotate) with the same vcf without encountering any problems.
I encountered an error while using the SnpSift caseControl command to analyze a VCF file. The error message is:
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 10
at org.snpsift.SnpSiftCmdCaseControl.annotate(SnpSiftCmdCaseControl.java:76)
at org.snpsift.SnpSiftCmdCaseControl.run(SnpSiftCmdCaseControl.java:411)
at org.snpsift.SnpSiftCmdCaseControl.run(SnpSiftCmdCaseControl.java:388)
at org.snpsift.SnpSift.run(SnpSift.java:588)
at org.snpsift.SnpSift.main(SnpSift.java:76)
The command that triggered this error is:
SnpSift caseControl -name "group1" "--0--000-0+++0-0-0-0-0+--0-++-0--0---+--0+0+-0+--+0--++0--0-00-++00++0+---+--0000++0+-0-+-++-0++000-0+00-000++-++-0-0--+-----0-+----0----++0-----0-0-0-0----00---+00--+---0++-00++--00++--0+0---+0-" input.vcf
The input VCF file contains 204 columns (with the standard header columns+my 195 samples), and I have verified the file is correctly formatted with no missing or malformed lines. I have previously used snpsift with other commands (like filter o annotate) with the same vcf without encountering any problems.