Python code to filter the VCF file with filter: 1000Gp1_AF < 0.05
Hi All, I will specifically looking for python code to extract this information from the below files.
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Brca1Reads
17 41245471 rs4986850 C T 140.34 PASS AC=0;AF=0.048;AN=2;ASP;BaseQRankSum=0.572;CAF=[0.9605,.,0.03949];CLNACC=RCV000111759.1,RCV000034730.2|RCV000047702.3|RCV000111758.2|RCV000120289.1|RCV000129094.1;CLNALLE=1,2;CLNDBN=Breast-ovarian_cancer\x2c_familial_1,not_provided|BRCA1_and_BRCA2_Hereditary_Breast_and_Ovarian_Cancer|Breast-ovarian_cancer\x2c_familial_1|AllHighlyPenetrant|Neoplastic_Syndromes\x2c_Hereditary;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet,.|GeneReviews:MedGen|GeneReviews:MedGen:OMIM:Orphanet|.|MedGen;CLNDSDBID=NBK1247:C2676676:604370:ORPHA145,.|NBK1247:C0677776|NBK1247:C2676676:604370:ORPHA145|.|C0027672;CLNHGVS=NC_000017.10:g.41245471C>A,NC_000017.10:g.41245471C>T;CLNORIGIN=1,3;CLNSIG=2,2|2|2|1|2;CLNSRC=ClinVar,Ambry_Genetics|ClinVar|Counsyl|.|GeneDx|Invitae;CLNSRCID=NM_007294.3:c.2077G>T,a42|NM_007294.3:c.2077G>A|46382|.|390598|4054;COMMON=1;ClippingRankSum=-1.067e+00;DP=374;FS=0.000;G5;GENEINFO=BRCA1:672;GNO;GQ_MEAN=22.35;GQ_STDDEV=28.56;HD;INT;InbreedingCoeff=0.2642;KGPROD;KGPhase1;LSD;MLEAC=2;MLEAF=0.032;MQ=60.00;MQ0=0;MQRankSum=0.00;NCC=1;NEGATIVE_TRAIN_SITE;NOC;NSM;OTH;OTHERKG;PH3;PM;PMC;POSITIVE_TRAIN_SITE;QD=14.03;REF;RS=4986850;RSPOS=41245471;RV;ReadPosRankSum=0.00;SAO=0;SLO;SNPEFF_AMINO_ACID_CHANGE=D397N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=9;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=BRCA1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000309486;SSR=0;VC=SNV;VLD;VP=0x050168080a15150517100110;VQSLOD=1.13;WGT=1;culprit=DP;dbNSFP_1000Gp1_AF=0.03983516483516483;dbNSFP_1000Gp1_AFR_AF=0.01016260162601626;dbNSFP_1000Gp1_AMR_AF=0.049723756906077346;dbNSFP_1000Gp1_ASN_AF=0.0;dbNSFP_1000Gp1_EUR_AF=0.08443271767810026;dbNSFP_RadialSVM_rankscore=0.41448;dbSNPBuildID=113 GT:AD:DP:GQ:PL 0/0:118,0:118:99:0,120,1800
17 41246481 rs1799950 T C 44.58 PASS AC=0;AF=0.016;AN=2;ASP;BaseQRankSum=-1.537e+00;CAF=[0.972,0.02801];CLNACC=RCV000034725.2|RCV000047326.3|RCV000111539.2|RCV000120281.1|RCV000132455.1;CLNALLE=1;CLNDBN=not_provided|BRCA1_and_BRCA2_Hereditary_Breast_and_Ovarian_Cancer|Breast-ovarian_cancer\x2c_familial_1|AllHighlyPenetrant|Neoplastic_Syndromes\x2c_Hereditary;CLNDSDB=.|GeneReviews:MedGen|GeneReviews:MedGen:OMIM:Orphanet|.|MedGen;CLNDSDBID=.|NBK1247:C0677776|NBK1247:C2676676:604370:ORPHA145|.|C0027672;CLNHGVS=NC_000017.10:g.41246481T>C;CLNORIGIN=1;CLNSIG=2|2|255|1|2;CLNSRC=Ambry_Genetics|ClinVar|Counsyl|.|GeneDx|Invitae;CLNSRCID=a992|NM_007294.3:c.1067A>G|45950|.|390328|14761;COMMON=1;ClippingRankSum=-4.060e-01;DP=366;FS=0.000;G5;GENEINFO=BRCA1:672;GNO;GQ_MEAN=20.53;GQ_STDDEV=22.05;HD;INT;InbreedingCoeff=-0.0568;KGPROD;KGPhase1;LSD;MLEAC=1;MLEAF=0.016;MQ=54.43;MQ0=0;MQRankSum=0.406;NCC=0;NEGATIVE_TRAIN_SITE;NOC;NSM;OTH;OTHERKG;PH3;PM;PMC;POSITIVE_TRAIN_SITE;QD=7.43;REF;RS=1799950;RSPOS=41246481;RV;ReadPosRankSum=-9.880e-01;SAO=0;SLO;SNPEFF_AMINO_ACID_CHANGE=Q309R;SNPEFF_CODON_CHANGE=cAg/cGg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=9;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=BRCA1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000493795;SSR=0;VC=SNV;VLD;VP=0x050168080a15150517100110;VQSLOD=-5.650e-01;WGT=1;culprit=DP;dbNSFP_1000Gp1_AF=0.027930402930402932,0.027930402930402932;dbNSFP_1000Gp1_AFR_AF=0.0040650406504065045,0.0040650406504065045;dbNSFP_1000Gp1_AMR_AF=0.049723756906077346,0.049723756906077346;dbNSFP_1000Gp1_ASN_AF=0.0,0.0;dbNSFP_1000Gp1_EUR_AF=0.05408970976253298,0.05408970976253298;dbNSFP_RadialSVM_rankscore=0.53344,0.53344;dbSNPBuildID=89 GT:AD:DP:GQ:PL 0/0:107,0:107:80:0,80,1800
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Why Python when better tools are available for the job?
The PyVCF library may be of help (https://github.com/jamescasbon/PyVCF)