https://info.gersteinlab.org/index.php?action=history&feed=atom&title=1000genomes_nonsyn 2026-05-16T15:35:42Z Revision history for this page on the wiki MediaWiki 1.42.6 https://info.gersteinlab.org/index.php?title=1000genomes_nonsyn&diff=57&oldid=prev 2010-06-09T12:00:10Z

<p>Created page with &#039;[http://homes.gersteinlab.org/people/suganthi/outbox/1000genomes/REL-0908/all_LOF/nsyn/CEU.0908.all.pc.nsyn CEU.0908.nsyn] Summary of file The pipeline software to map SNPs on…&#039;</p> <p><b>New page</b></p><div>[http://homes.gersteinlab.org/people/suganthi/outbox/1000genomes/REL-0908/all_LOF/nsyn/CEU.0908.all.pc.nsyn CEU.0908.nsyn]<br /> <br /> <br /> Summary of file<br /> <br /> The pipeline software to map SNPs on to the human genome was written by Lukas Habegger and analysis by Suganthi Balasubramanian, Yale University.<br /> The SNPs are mapped based on GENCODE ver3b annotation file.<br /> <br /> <br /> Input files used and other notes:<br /> <br /> Gene annotation file GENCODE ver3b downloaded from<br /> ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/gencode.v3b.annotation.NCBI36.gtf.gz<br /> <br /> SNPs mapped to protein-coding transcript annotations of the GENCODE file<br /> Amino acid translations done with respect to reference allele in the human genome (not ancestral allele)<br /> <br /> SNP call sets<br /> <br /> 1. Pilot1 Low coverage Chromosome 20, Broad call set downloaded from<br /> <br /> http://www.broadinstitute.org/~jmaguire/pilot1_chr20.august_31_2009/release.1/<br /> <br /> High stringency SNP calls used.<br /> <br /> <br /> 2. Pilot1 Low coverage Chromosome 20, Univ. of Michigan call set downloaded from<br /> <br /> server: fantasia.sph.umich.edu<br /> user: 1000genomes<br /> pwd: (ask for password if needed)<br /> <br /> dir: pub/2009.08.chr20.2<br /> <br /> The specific SNP files used as input for pipeline are:<br /> CEU.ref_called_allels<br /> CHB+JPT.ref_called_allels<br /> YRI.ref_called_allels<br /> <br /> SNPs where either allele does not match the reference genome have not been included. <br /> <br /> <br /> 3. Genome-wide Pilot1 Low coverage call set from Richard Durbin&#039;s group downloaded from<br /> <br /> ftp://ftp.sanger.ac.uk/pub/1000genomes/REL-0908/LowCov/<br /> <br /> Only high quality SNPs from Richard&#039;s set have been used (lines where filter field column7=0)</div>

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