issue converting VEP.vcf file to maf

[iichelhadi]

Hi all I have a VEP annotated vcf file. The annotation was done using VEP v103 with GRCh38 genome build. When I run the following code perl vcf2maf.pl --input-vep 1880_somatic.filtered.VEP.vcf --output-maf 1880.maf --tumor-id 1880_T --normal-id 1880_N --vcf-tumor-id 1880_T --vcf-normal-id 1880_N I get a long output as follows:

Use of uninitialized value $effect in string eq at vcf2maf.pl line 801, <GEN1> line 4960.
Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 802, <GEN1> line 4960.
Use of uninitialized value $effect in string eq at vcf2maf.pl line 803, <GEN1> line 4960.
Use of uninitialized value $effect in string eq at vcf2maf.pl line 804, <GEN1> line 4960.
Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 805, <GEN1> line 4960.
Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 806, <GEN1> line 4960.
Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 807, <GEN1> line 4960.
Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 808, <GEN1> line 4960.
Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 809, <GEN1> line 4960.
Use of uninitialized value $effect in string eq at vcf2maf.pl line 810, <GEN1> line 4960.
Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 811, <GEN1> line 4960.
Use of uninitialized value $effect in string eq at vcf2maf.pl line 812, <GEN1> line 4960.
Use of uninitialized value $effect in string eq at vcf2maf.pl line 813, <GEN1> line 4960.

Please help. Any advice would be greatly appreciated.

[xuexidaima]

Is it sloved now? i met the same question

[iichelhadi]

I managed to solve the issue for myself. I annotated the vcfs with VEP without using vcf2maf and then used vcf2maf with the argument --inhibit-vep to run the conversion to maf.

perl vcf2maf.pl --inhibit-vep \
        --input-vcf somatic.VA.VEP.vcf \
        --output-maf MAF.maf \
        --tumor-id tumor_T \
        --normal-id normal_N \
        --ref-fasta hg38.fa \
        --ncbi-build hg38 \
        --verbose

hope this helps.

[shzyjbren]

Hi，

I run the following code. And I found the MuTect2.maf file was the same as the MuTect2.vep.maf file. While using --inhibit-vep parameter ,It is found that the dbSNP_RS column seems inaccurate.

Do you have similar problems？

#vcfs without using vep 
perl vcf2maf.pl \
        --input-vcf MuTect2.vcf \
        --output-maf MuTect2.maf \
        --ncbi-build GRCh37 \
        --tumor-id BJS_1_T \
        --normal-id BJS_1_N &&\

#vcfs with using VEP
perl vcf2maf.pl \
        --input-vcf MuTect2.vep.vcf \
        --output-maf MuTect2.vep.maf \
        --ncbi-build GRCh37 \
        --tumor-id BJS_1_T \
        --normal-id BJS_1_N &&\

#vcfs with using VEP
#vcf2maf with the argument --inhibit-vep
perl vcf2maf.pl --inhibit-vep \
        --input-vcf MuTect2.vep.vcf \
        --output-maf MuTect2.vep.inhibit_vep.maf \
        --ncbi-build GRCh37 \
        --tumor-id BJS_1_T \
        --normal-id BJS_1_N &&