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ylab-hi / ScanNeo

A pipeline for identifying indel derived neoantigens using RNA-Seq data
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empty vcf file in step2 anno #5

Closed eunjeongcho closed 3 years ago

eunjeongcho commented 3 years ago

Hi. @dolittle007 Thanks for the good program.

I have a question about step2 anno. As a result of step2, an empty vcf file was created. I found there was no variant in the pre_vep.44778.vcf file. The same problem repeats with the "-s" option. How can I solve this problem?

my input vcf looks like this. Thanks.

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT input

1 979487 . A AG . . NS=1;AO=4;DP=11;AB=0.36;SVLEN=1;SVTYPE=INS;SVMETHOD=transIndel_ALN;CHR2=1;END=979488 GT 1/1 1 983154 . . . . NS=1;AO=11;DP=11;AB=1.0;SVLEN=1;SVTYPE=DEL;SVMETHOD=transIndel_ALN;CHR2=1;END=983155 GT 1/1 1 1477323 . . . . NS=1;AO=29;DP=29;AB=1.0;SVLEN=2;SVTYPE=DEL;SVMETHOD=transIndel_ALN;CHR2=1;END=1477325 GT 1/1

dolittle007 commented 3 years ago

Can you try to run the following command in your bash environment? I assume you are using the GRCh38 reference.

vep --offline --force_overwrite --assembly GRCh38 --input_file INPUT_VCF --format vcf --output_file OUTPUT_VCF \ --vcf --symbol --terms SO --af --af_gnomad --plugin Downstream --plugin Wildtype --no_stats`

OR you can set -c 1 when using "ScanNeo anno" to see whether it will output variants or not. Thank you.

eunjeongcho commented 3 years ago

There seems to be a problem with my ref or gtf file, so I downloaded the reference and gtf again from genecode and the problem was solved. Thank you.