T. cristinae llinkage map with LM2 and 2nd Dovetail assembly

Post date: Jun 13, 2016 3:14:20 AM

perl ../scripts/makeMultiFamLinkage.pl offspringGenotypesfamA.txt offspringGenotypesfamB.txt offspringGenotypesfamC.txt

This generates lm_tcrist.txt, which includes one families,

116 individuals (191 offspring, 6 parents) and 17,478 SNPs.

java -cp ~/source/lepmap2/bin/ Filtering data=lm_tcrist.txt epsilon=0.01 dataTolerance=0.005 missingLimit=10 keepAlleles=1 > data_tcristlm.txt

***

Mendel error statistics:

0->0 : 0

0->1 : 0

0->2 : 0

Error rate = 0.0

1->0 : 0

1->1 : 0

1->2 : 0

Error rate = 0.0

2->0 : 0

2->1 : 0

2->2 : 0

Error rate = 0.0

0,2->0,2 : 1598324

0,2->1 : 0

1,2->1,2 : 0

1,2->0 : 0

Error rate = 0.0

***

Filtering markers based on segregation distortion

Removed 11546 markers from family famA

( from which 4884 due to missing parent genotypes, run ParentCall to fix the parents )

Removed 13523 markers from family famB

( from which 12426 due to missing parent genotypes, run ParentCall to fix the parents )

Removed 16870 markers from family famC

( from which 16598 due to missing parent genotypes, run ParentCall to fix the parents )

Maternally informative markers = 4312 (of 17478)

Paternally informative markers = 5989

Maternally or paternally informative markers = 9893

***

java -cp ~/source/lepmap2/bin/ SeparateChromosomes data=data_tcristlm.txt lodLimit=4 sizeLimit=50 > lgs_tcrist.txt

LOD 4: Number of LGs = 12, markers in LGs = 6873, singles = 10605

LOD 5: Number of LGs = 19, markers in LGs = 5927, singles = 11551

LOD 6: Number of LGs = 21, markers in LGs = 5800, singles = 11678

LOD 7: Number of LGs = 21, markers in LGs = 5716, singles = 11762

LOD 8: Number of LGs = 22, markers in LGs = 5532, singles = 11946

LOD 9: Number of LGs = 23, markers in LGs = 5187, singles = 12291

LOD 10: Number of LGs = 23, markers in LGs = 5004, singles = 12474

LOD 15: Number of LGs = 22, markers in LGs = 3344, singles = 14134

## using LOD 4

java -cp ~/source/lepmap2/bin/ JoinSingles lgs_tcrist.txt data=data_tcristlm.txt lodLimit=3 lodDifference=2 > lgs_tcrist_js.txt

joined 616 single markers, non-conflicting LOD score > 3.490038550540774

Number of LGs = 12, markers in LGs = 7572, singles = 9906

5. Assign (or unassign) entire scaffolds (including male informative markers) to LGs. I modified the script on June 28th, 2016. Now $alt is the proportion of the second most common LG relative to the most common LG. So, if the second best LG is support by > 50% as many SNPs as the best LG, the scaffold is not assigned a LG.

Combine map and scaffold data

map<-read.table("femLgsJs_lyclm.txt",header=FALSE)

snps<-read.table("combinedSnpList.txt",header=FALSE)

o<-cbind(map,snps)

colnames(o)<-c("flg","scaf","pos")

write.table(o,"tcrLgs.txt",row.names=FALSE,col.names=TRUE,quote=FALSE)

Run perl script

## key params ##

## decide on LG for scaf

## rules:

## $nsnp SNPs supporting LG with $prct of SNPs in agreement

## $min SNPs total

## $alt is maximum % for an alternative LG

$prct = 0.1;

$nsnp = 2;

$min = $nsnp;

$alt = 0.5;

#############

perl assignScafFilter.pl tcrLgs.txt

assigned LGs for 237 scaffolds (89% of SNPs), failed to assign LGs for 298 scaffolds

tail -n +2 mod_tcrLgs.txt | cut -f 1 -d " " > mod_tcrLgsSnp.txt

6. Run order chromosome, use all three families and run one chromosome at a time for speed.

perl wrap_qsub_slurm_orderScafs.pl