Am trying to read in a vcf file to R. The vcf is from the 1000 G project here -
so the code
library(VariantAnnotation) ScanVcfParam(info=c("EAS_AF","EUR_AF","AFR_AF","AMR_AF","SAS_AF","CSQ"))->param readVcf("ALL.chr2.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.annotation.vcf.gz","hg19",param=param)->cff length((info(cff)[["CSQ"]]))
The original vcf file has a column with the position (POS) col 2 - however, that is not accessible in the file afterwards.
info(header(cff)): Number Type Description CIEND 2 Integer Confidence interval around END for impreci... CIPOS 2 Integer Confidence interval around POS for impreci... CS 1 String Source call set. END 1 Integer End coordinate of this variant IMPRECISE 0 Flag Imprecise structural variation MC . String Merged calls. MEINFO 4 String Mobile element info of the form NAME,START... MEND 1 Integer Mitochondrial end coordinate of inserted s... MLEN 1 Integer Estimated length of mitochondrial insert MSTART 1 Integer Mitochondrial start coordinate of inserted... SVLEN . Integer Difference in length between REF and ALT a... SVTYPE 1 String Type of structural variant TSD 1 String Precise Target Site Duplication for bases,... AC A Integer Total number of alternate alleles in calle... AF A Float Estimated allele frequency in the range (0,1) NS 1 Integer Number of samples with data AN 1 Integer Total number of alleles in called genotypes EAS_AF A Float Allele frequency in the EAS populations ca...# EUR_AF A Float Allele frequency in the EUR populations ca...# AFR_AF A Float Allele frequency in the AFR populations ca...# AMR_AF A Float Allele frequency in the AMR populations ca...# SAS_AF A Float Allele frequency in the SAS populations ca...# DP 1 Integer Total read depth AA 1 String Ancestral Allele. Format: AA|REF|ALT|Indel... CSQ . String Consequence type as predicted by VEP WITH ...# GENCODE . String The annotation of coding variants and spli...# ALOFT A String The Annotation Of Loss-of-Function Transcr...# PHOSPHORYLATION A String Predicted as phosphorylation sites by Phos... ERB . String Ensembl Regulatory Build. Format: Allele|G... HighD . String The Super population with the higher deriv...# FUNSEQ A Float FunSeq score for noncoding SNV
prints a list of parameters to do a selection on. However, the POS column is not among them. How can I get the positions of all the variants in the vcf?