Sib-pair Command: read chain


ClassData Declaration command
Nameread chain
Arguments <chain file name>

Read in the specified UCSC chain file and update the map positions of currently active loci using that information.

Example:

#
# Liftover from build 38 to build 37
#
>> read chain ~/Genetics/Maps/hg38ToHg19.over.chain.gz
Reading chain file "/home/davidD/Genetics/Maps/hg38ToHg19.over.chain.gz".

Lifted over 35727 (100.0%) map positions.

#
# Check that map is consistent with b37 external data
#
>> test map ~/Genetics/Maps/UK10K_COHORT.20160215.sites.vcf.gz

Comparing current map to "/home/davidD/Genetics/Maps/UK10K_COHORT.20160215.sites.vcf.gz".
Reference Seq = ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
[...]
Number of markers Sib-pair map  = 35727
Number of markers external map  = 46671335
Total number intersecting       = 3827 (0.107, 0.000)
Intersecting on marker name     = 1941 (discordant position=0)
Intersecting on map position    = 3827 (discordant name=1886)
Number where multiple matches   = 47
Number unique to Sib-pair map   = 31900

>> sum tab

Test: "map comparison 1=name 2=pos 3=perfect 4=dups".

Category     Count Percent
---------- ------- -------
0            31900    89.3
2=pos         1852     5.2
3=perfect     1929     5.4
4=dups          46     0.1

See also:

read mapread map, guessing format incl GTF, VCF
show mapshow linkage map


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