I'm using 1000Genomes to obtain the complete genome for each chromosome for European individuals. I've gotten the bam files from the individuals, got the bed and fasta files from the bam files, and used those to construct their chromosomes. So far, however, I've only used exome data: IE) ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12348/exome_alignment/NA12348.chrom20.ILLUMINA.bwa.CEU.exome.20121211.bam
from site: http://www.1000genomes.org/data-portal/sample/NA12348
which I don't believe gives me all the SNPs in the full genome. So I'm looking to use complete genome or low coverage WGS data. I'm not sure which bam file will give me the data I'm looking for. For complete genomics, there's this file: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12348/cg_data/NA12348_lcl_SRR822975.mapped.COMPLETE_GENOMICS.CGworkflow2_2_evidenceOnly.CEU.high_coverage.20130401.bam
Which has the name 'evidenceOnly'. There is a similar file with the name 'evidenceSupport'. What is the difference between the two? More generally, which bam file would suit what I'm looking for?
