Add more gene annotations

[tavinathanson]

Consider adding more annotation information, depending on the direction we want to take CycleDash.

(Or allowing for plugins with this information.)

For example, @timodonnell talking about UCSC:

it can pull in COSMIC and other annotations, as well as run some standard tools to predict things like severity of change

Uploaded Variation    Location    Allele    Gene    Feature    Feature type    Consequence    Position in cDNA    Position in CDS    Position in protein    Amino acid change    Codon change    Co-located Variation    Extra
chr1_12907620_A/G    chr1:12907620    G    B7ZW38    uc009vno.2    Transcript    synonymous_variant    618    523    175    L/L    Ttg/Ctg    rs2994092    EXON=1/1
chr1_12907620_A/G    chr1:12907620    G    O60812    uc010obf.2    Transcript    synonymous_variant    749    523    175    L/L    Ttg/Ctg    rs2994092    EXON=2/2
chr1_12920891_G/T    chr1:12920891    T    O60811    uc001aum.1    Transcript    intron_variant    -    -    -    -    -    rs1856643    INTRON=3/3
chr1_12920892_G/T    chr1:12920892    T    O60811    uc001aum.1    Transcript    intron_variant    -    -    -    -    -    rs1856644    INTRON=3/3
chr1_16896120_G/C    chr1:16896120    C    Q3BBV0    uc001ayw.4    Transcript    intron_variant    -    -    -    -    -    rs4098011    INTRON=22/28
chr1_16896120_G/C    chr1:16896120    C    Q8IX71    uc009vot.1    Transcript    intron_variant    -    -    -    -    -    rs4098011    INTRON=7/10
chr1_16896120_G/C    chr1:16896120    C    A6NDD8    uc001ayz.1    Transcript    intron_variant    -    -    -    -    -    rs4098011    INTRON=7/10
chr1_16896120_G/C    chr1:16896120    C    Q3BBV0    uc010oce.1    Transcript    intron_variant    -    -    -    -    -    rs4098011    INTRON=12/14

that's an example table it makes

[timodonnell]

I was using UCSC's "variant annotation integrator"

http://www.noncode.org/cgi-bin/hgVai

On Tue, Feb 10, 2015 at 3:53 PM, Tavi Nathanson [email protected] wrote:

Consider adding more annotation information, depending on the direction we want to take CycleDash.

(Or allowing for plugins with this information.)

For example, @timodonnell https://github.com/timodonnell talking about UCSC:

standard tools to predict things like severity of change

Uploaded Variation Location Allele Gene Feature Feature type Consequence
Position in cDNA Position in CDS Position in protein Amino acid change
Codon change Co-located Variation Extra
chr1_12907620_A/G chr1:12907620 G B7ZW38 uc009vno.2 Transcript
synonymous_variant 618 523 175 L/L Ttg/Ctg rs2994092 EXON=1/1
chr1_12907620_A/G chr1:12907620 G O60812 uc010obf.2 Transcript
synonymous_variant 749 523 175 L/L Ttg/Ctg rs2994092 EXON=2/2
chr1_12920891_G/T chr1:12920891 T O60811 uc001aum.1 Transcript
intron_variant - - - - - rs1856643 INTRON=3/3
chr1_12920892_G/T chr1:12920892 T O60811 uc001aum.1 Transcript
intron_variant - - - - - rs1856644 INTRON=3/3
chr1_16896120_G/C chr1:16896120 C Q3BBV0 uc001ayw.4 Transcript
intron_variant - - - - - rs4098011 INTRON=22/28
chr1_16896120_G/C chr1:16896120 C Q8IX71 uc009vot.1 Transcript
intron_variant - - - - - rs4098011 INTRON=7/10
chr1_16896120_G/C chr1:16896120 C A6NDD8 uc001ayz.1 Transcript
intron_variant - - - - - rs4098011 INTRON=7/10
chr1_16896120_G/C chr1:16896120 C Q3BBV0 uc010oce.1 Transcript
intron_variant - - - - - rs4098011 INTRON=12/14

that's an example table it makes

—
Reply to this email directly or view it on GitHub
https://github.com/hammerlab/cycledash/issues/447.

[danvk]

@armish Is this done now?

[armish]

this is partially addressed by PR https://github.com/hammerlab/cycledash/pull/750; but we probably have to be more specific about the annotations we want -- maybe we can enter them as separate issues and close this one down.