| Class | Data Declaration command |
| Name | read 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 map | read map, guessing format incl GTF, VCF |
| show map | show linkage map |
| << (read map) | Up to index | >> (read statistics) |