Merge pull request #19 from lh3/readme-male

README: remove PARs for males

README.md

@@ -7,7 +7,7 @@ cd hickit-0.1_x64-linux
 # Map Dip-C reads and extract contacts (skip if you use your own pipeline)
 ./seqtk mergepe read1.fq.gz read2.fq.gz | ./pre-dip-c - | bwa mem -5SP -p hs37d5.fa - | gzip > aln.sam.gz
 ./k8 hickit.js vcf2tsv phased.vcf > phased_SNP.tsv   # extract phased SNPs from VCF
-./k8 hickit.js sam2seg -v phased_SNP.tsv aln.sam.gz | ./k8 hickit.js chronly - | gzip > contacts.seg.gz # for male
+./k8 hickit.js sam2seg -v phased_SNP.tsv aln.sam.gz | ./k8 hickit.js chronly - | ./k8 hickit.js bedflt par.bed - | gzip > contacts.seg.gz # for male
 #./k8 hickit.js sam2seg -v phased_SNP.tsv aln.sam.gz | ./k8 hickit.js chronly -y - | gzip > contacts.seg.gz # for female
 ./hickit -i contacts.seg.gz -o - | bgzip > contacts.pairs.gz  # optional
 
@@ -174,7 +174,7 @@ hickit -i contacts.seg.gz -o - | bgzip > contacts.pairs.gz
 When you have phased SNPs in VCF, you can generate contact pairs with the phase columns
 ```sh
 hickit.js vcf2tsv NA12878_phased.vcf.gz > phased_SNP.tsv
-hickit.js sam2seg -v phased_SNP.tsv aln.sam.gz | hickit.js chronly - | gzip > contacts.seg.gz
+hickit.js sam2seg -v phased_SNP.tsv aln.sam.gz | hickit.js chronly - | hickit.js bedflt par.bed - | gzip > contacts.seg.gz
 hickit -i contacts.seg.gz -o - | bgzip > contacts.pairs.gz
 ```
 where `hickit.js chronly` filters out non-chromosomal contigs and
@@ -184,7 +184,7 @@ chr1    1010717 C       T
 chr1    1011531 T       C
 chr1    1013136 C       G
 ```
-Note that the above is for **male** samples. For **female** samples, the part `hickit.js chronly -` should be replaced by `hickit.js chronly -y -` to remove the Y chromosome.
+Note that the above is for **male** samples. Here the pseudoautosomal regions (PARs, coordinates supplied in `par.bed`) are excluded from analysis. For **female** samples, the part `hickit.js chronly - | hickit.js bedflt par.bed -` should be replaced by `hickit.js chronly -y -` to remove the Y chromosome instead.
 
 ### <a name="impute"></a>Imputing missing phases (diploid single-cell Hi-C only)