Question

How to add protein ID transcript ("NP_")?

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8.0 years ago

agata88 ▴ 870

Hi all,

I would like to add "NP_" number to snp variants. I am using SnpEff and SnpSift.

I was using command below to annotate variants to hg19:

java -jar snpEff.jar -v -canon hg19 test_2.vcf > test_3.vcf

Output vcf includes NM number (transcript ID) but no protein number (NP).

Any idea how to add this?

Best,

Agata

next-gen annotation • 2.6k views

ADD COMMENT • link updated 8.0 years ago by Pierre Lindenbaum 161k • written 8.0 years ago by agata88 ▴ 870

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Mapping refseq transcripts to encoded proteins (NM_ to NP_)

How To Transfer Gene Id Into Protein Id

ADD REPLY • link 8.0 years ago by Sukhi Singh 11k

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Thanks, but I was wondering how to do that using SnpEff or SnpSift ...

ADD REPLY • link 8.0 years ago by agata88 ▴ 870

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Ahh, wait for someone more experienced with that then :)

ADD REPLY • link 8.0 years ago by Sukhi Singh 11k

score 2 · Answer 1 · 2016-04-08

first check snpeff is not able to print the NP_*

the ugly way: extract the NMs from your VCF, get the NP_ with NCBI efetch and create a sed file appending the NP to the NM...

 curl -Ls "https://raw.githubusercontent.com/arraytools/vc-annotation/master/snpeff/tmp/nonsyn_splicing.vcf" | grep -v "##" |\
cut -f 8 | tr ";" "\n" | grep "^ANN=" | tr "|" "\n" | grep "^NM_*" | while read S;\
do
       curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=${S}&rettype=gbc" |\
       xmllint --xpath '//INSDQualifier_name[.="protein_id"]/../INSDQualifier_value/text()' - |\
       awk -v NM=${S}  '{printf("s/|%s|/|%s|%s|/g\n",NM,NM,$1);}'  ; 
done > out.sed

then use this sed file to append the NP to the NM:

$ curl -Ls "https://raw.githubusercontent.com/arraytools/vc-annotation/master/snpeff/tmp/nonsyn_splicing.vcf" | sed -f out.sed | grep NP_ | head


1   1014228 COSM3751464 G   A   11.4963 PASS    DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=50;GENE=ISG15;ANN=A|missense_variant|MODERATE|ISG15|ISG15|transcript|NM_005101.3|NP_005092.1|protein_coding|2/2|c.248G>A|p.Ser83Asn|355/666|248/498|83/165||   GT:PL   0/1:39,3,0
1   21850165    .   A   T   4.88476 PASS    DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=50;ANN=T|missense_variant|MODERATE|HSPG2|HSPG2|transcript|NM_001291860.1|NP_001278789.1|protein_coding|57/97|c.7325T>A|p.Ile2442Asn|7405/14343|7325/13179|2442/4392||  GT:PL   0/1:31,3,0
1   27793570    .   G   A   5.58414 PASS    DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=50;ANN=A|missense_variant|MODERATE|STX12|STX12|transcript|NM_177424.2|NP_803173.1|protein_coding|3/9|c.226G>A|p.Glu76Lys|351/3079|226/831|76/276|| GT:PL   0/1:32,3,0
1   114720652   COSM4218186 G   A   13.3811 PASS    DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=50;GENE=CSDE1;ANN=A|stop_gained|HIGH|CSDE1|CSDE1|transcript|NM_001242891.1|NP_001229820.1|protein_coding|18/21|c.2077C>T|p.Gln693*|2599/4313|2077/2535|693/844||;LOF=(CSDE1|CSDE1|1|1.00);NMD=(CSDE1|CSDE1|1|1.00) GT:PL   0/1:41,3,0
1   153986128   .   A   G   10.9943 PASS    DP=2;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=50;ANN=G|missense_variant|MODERATE|RAB13|RAB13|transcript|NM_002870.3|NP_002861.1|protein_coding|1/8|c.109T>C|p.Tyr37His|250/1235|109/612|37/203||   GT:PL   1/1:38,3,0
1   173485410   COSM5378456 C   T   6.32957 PASS    DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=50;GENE=PRDX6;ANN=T|missense_variant|MODERATE|PRDX6|PRDX6|transcript|NM_004905.2|NP_004896.1|protein_coding|3/5|c.302C>T|p.Pro101Leu|353/1670|302/675|101/224||    GT:PL   0/1:33,3,0
1   183116645   .   A   T   7.93884 PASS    DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=50;ANN=T|missense_variant|MODERATE|LAMC1|LAMC1|transcript|NM_002293.3|NP_002284.3|protein_coding|7/28|c.1397A>T|p.Lys466Ile|1654/7889|1397/4830|466/1609|| GT:PL   0/1:35,3,0
1   228097438   .   T   C   7.93884 PASS    DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=50;ANN=C|missense_variant|MODERATE|ARF1|ARF1|transcript|NM_001024226.1|NP_001019397.1|protein_coding|3/5|c.245T>C|p.Phe82Ser|473/1973|245/546|82/181|| GT:PL   0/1:35,3,0
1   235246483   .   G   C   6.32957 PASS    DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=50;ANN=C|missense_variant|MODERATE|ARID4B|ARID4B|transcript|NM_001206794.1|NP_001193723.1|protein_coding|7/24|c.383C>G|p.Pro128Arg|760/5946|383/3939|128/1312||    GT:PL   0/1:33,3,0
10  73913343    COSM4144861 T   C   9.6729  PASS    DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=50;GENE=PLAU;ANN=C|missense_variant|MODERATE|PLAU|PLAU|transcript|NM_002658.3|NP_002649.1|protein_coding|6/11|c.422T>C|p.Leu141Pro|568/2377|422/1296|141/431|| GT:PL   0/1:37,3,0