User Manual

User Manual

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LDx measures linkage disequilbrium from high-throughput pooled resequencing data. It is implemented as a perl script, and should work with any operating system with Perl. Details can of the method are described in "LDx: estimation of linkage disequilibrium from high-throughput pooled resequencing data"

Usage

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Inputs

LDx has two mandatory arguments, and several options. In the default, they are calibrated to work with 40x coverage 93 bp reads with gap lengths of 150 bp. It will be important to consider the read depth and size length arguments when using the program, and the PHRED quality score cut offs and allele frequency cut offs can be modified to expand search results.

Please note, the options must come before the input.sam and snplist.vcf

\$ ./LDx.pl [options] input.sam snplist.vcf

input.sam - Sorted, duplicates removed .sam file of a single chromosome
snplist.vcf - VCF file of probable SNP locations. snplist.vcf MUST be sorted.

Flag Function Default Restrictions
-l Minimum read depth 10 >0
-h Maximum read depth (to prevent the inclusion of repeats) 100 >0
-s Read from one end of paired end read to the other (i.e., distance between start of first read to end of second read) 500 >0
-q PHRED quality score cut off 20 1-46
-a Allele frequency cut offs 0.1 [0,1]
-i Minimum intersection depth 11 >0

Interpreting Outputs

The output of LDx returns will be piped to standard out for your own redirection. For every pair of SNPs identified, information will be printed with reference to the following 2x2 haplotype tape.

SNP1 = A/a
SNP2 = B/b
B b
A x_11 x_21
a x_12 x_22

Note, the allele labels are assigned such that A and B always represent the major allele at their respective loci.

OUTPUT:

Location of SNP1
Location of SNP2
Number of pairs observed with x_11
Number of pairs observed with x_12
Number of pairs observed with x_21
Number of pairs observed with x_22
Estimate for allele frequency of allele A
Estimate for allele frequency of allele B
Read depth for SNP1
Read depth for SNP2
Intersecting read depth
Approx MLE R2 (low end of interval)
Approx MLE estimate
Approx MLE (high end of interval)
Direction Computation R2
A
a *
B
b

Support and Feedback

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Please contact Alison Feder (afeder@stanford.edu) with any questions, comments or concerns.

*Note, a previous version of this manual incorrectly listed these four entries as A B a b, not A a B b