Hg19 Bed File Compatible With Gatk

Question

[kanwarjag]

What will be the best source to download a bed file of hg19 annotation compatible with GATK. USCS browser http://genome.ucsc.edu/cgi-bin/hgTables?command=start and Biomart can be used. However Ensemble chr need to be modified. I need a bed file with chr, start, end, strand, gene name, Enetrz id (at least) Thanks

Answer 1

[Pierre Lindenbaum]

• remove the chromosome prefix 'chr'
• change some names (see my post : "g1kv37 vs hg19 " http://plindenbaum.blogspot.fr/2013/07/g1kv37-vs-hg19.html )

or simpler: just use ensembl biomart to download the bed file: chr, start, end, strand, gene name, Entrez id