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Question: SPV/DP in vcf annotation_whole exome data
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gravatar for shimonabiswas
2.7 years ago by
shimonabiswas • 0
shimonabiswas • 0 wrote:

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!
sequencing snp • 581 views
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modified 2.7 years ago • written 2.7 years ago by shimonabiswas • 0
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gravatar for h.mon
2.7 years ago by
h.mon ♦ 32k
Brazil
h.mon ♦ 32k wrote:

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?
ADD COMMENT • link modified 2.7 years ago • written 2.7 years ago by h.mon ♦ 32k

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.

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by shimonabiswas • 0
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