SPV/DP in vcf annotation_whole exome data

Question

[shimonabiswas]

Hi folks, I have just begun looking at vcf annotated files, from whole exome sequencing (snps and indels mostly). Vcf files show SPV=n / DP=n; what do these numeric values indicate?

Also I have some descriptions with each SNP - "modifier", "moderate", "high" and "low". What do these terms indicate?

All explanations welcome!

Answer 1

[h.mon]

Which program was used for variant calling?

SPV - somatic_p_value SPV (col 8) Somatic p-value for Somatic/LOH events

DP - DP (Integer): Read depth at this position for this sample.

Also I have some descriptions with each SNP - "modifier", "moderate", "high" and "low".

Examples?

[shimonabiswas]

Thanks h.mon! not sure but maybe samtools for variant calls. Here are some examples

missense_variant MODERATE synonymous_variant LOW intron_variant MODIFIER sequence_feature LOW stop_gained HIGH

not sure what "modifier" indicates, eg row 3 intron variant should really have no modification effect at transcript/ protein levels.