SNPEff error message!

[shyam_la]

I have been trying to use the latest build of SNPEff to annotate a mutation list that I have. The input is a tab delimited text file with columns as recommended by the SNPEff faq page.. chromosome_name, chromosome_position, reference sequence, changed sequence: A slash is used to separate two alleles

I don't understand what the error is (it just says error warnings and then types out the whole variants file and terminates) or what needs to be corrected. Any ideas?


Shyam Sundar@HH200-PC /cygdrive/i/exome/snpeff
$ java -Xmx8g -jar snpeff.jar hg19m data/variants.txt
##SnpEffVersion="2.1b (build 2012-04-20), by Pablo Cingolani"
##SnpEffCmd="SnpEff hg19m data/variants.txt "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this vari ant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Ac id_change | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | W ARNINGS ] )' ">
0 . . . . .
1 1247305 C T . . . .
1 1328643 G A . . . .
1 1394674 C T . . . .
1 1560870 C T . . . .
1 1601021 G A . . . .
1 1653142 G A . . . .
1 1891342 G A . . . .
1 2408160 G T . . . .
1 2527562 G A . . . .
1 2527593 G A . . . .
1 2938776 C T . . . .
1 2939346 G A . . . .
1 4829814 C T . . . .
1 4834669 C T . . . .
1 6150453 G T . . . .
1 6158499 C T . . . .
1 6215565 C T . . . .
1 6529233 C T . . . .
1 6535136 G A . . . .
1 9164636 G A . . . .
1 11129576 C T . . . .
1 11217165 G A . . . .
1 11272348 C T . . . .
1 12888587 C T . . . .
1 12900489 C T . . . .
1 12908101 C T . . . .
1 13173032 C T . . . .
1 15361402 C T . . . .
1 15769993 G A . . . .
1 15802897 T C . . . .
1 16057666 C T . . . .
1 16383230 C T . . . .
1 16893612 G A . . . .
1 16934992 G A . . . .
1 17046682 A C . . . .
1 17275337 C T . . . .
1 21226201 G A . . . .
1 22332414 G A . . . .
1 24685062 C T . . . .
1 25290902 G A . . . .
1 25611220 C T . . . .
1 26383928 G A . . . .
1 27687372 G A . . . .
1 29652037 C T . . . .
1 32130882 G A . . . .
1 32134508 C T . . . .
1 32740713 G A . . . .
1 33361118 G A . . . .
1 33958820 C T . . . .
1 34006125 G A . . . .
1 34123714 C T . . . .
1 34330204 G A . . . .
1 35365303 G A . . . .
1 35919951 G A . . . .
1 36786593 C T . . . .
1 38048424 G A . . . .
1 39305387 G A . . . .
1 39696981 C T . . . .
1 40230478 C T . . . .
1 40737739 C T . . . .
1 42875654 G A . . . .
1 43223590 C T . . . .
1 43357241 T A . . . .


PS: hg19m is a custom genome I built for SNPEff, to match the original reference file I used. I am using refseq genes to build..

[shyam_la]

Had to use "-i txt -o txt" in the command line as the default accepted input format is .vcf...

This is resolved!!