10. Merging of Duplicate Cases

To take full advantage of the duplicates samples in our dataset, we merged the respective counterparts.

Merges BAMs:

SampleNames="AfricanOwl_01 Archangel_01 BerlinLongFacedTumbler_01 BirminghamRoller_01 Carneau_01 Cumulet_01 EgyptianSwift_01 EnglishTrumpeter_01 FeralUT_01 IndianFantail_01 IndianFantail_02 IranianTumbler_01 Jacobin_01 Laugher_01 Lebanon_01 MarcheneroPouter_01 Mookee_01 OrientalRoller_01 ParlorRoller_01 RacingHomer_01 SaxonMonk_01 Shakhsharli_01 SyrianDewlap_01"
WGS="~/data/Pigeons/Analysis/PaleoMix_Re-Sequencing/"
GBS="~/data/Pigeons/Analysis/PaleoMix_GBS/"
Pairs="~/data/Pigeons/Analysis/Samtools_WGS-GBS/"

for query in $SampleNames
do
    echo samtools merge ${Pairs}/${query}-WGS-GBS.RockDove_DoveTail_ReRun.realigned.bam ${WGS}/${query}-WGS.RockDove_DoveTail_ReRun.realigned.bam ${GBS}/${query}-GBS.RockDove_DoveTail_ReRun.realigned.bam
    
done | xsbatch -c 1 -R --max-array-jobs 25 --mem-per-cpu 7000 -J Pairs --time 1-00 --

Indexes BAMs:

SampleNames="AfricanOwl_01 Archangel_01 BerlinLongFacedTumbler_01 BirminghamRoller_01 Carneau_01 Cumulet_01 EgyptianSwift_01 EnglishTrumpeter_01 FeralUT_01 IndianFantail_01 IndianFantail_02 IranianTumbler_01 Jacobin_01 Laugher_01 Lebanon_01 MarcheneroPouter_01 Mookee_01 OrientalRoller_01 ParlorRoller_01 RacingHomer_01 SaxonMonk_01 Shakhsharli_01 SyrianDewlap_01"
WGS="~/data/Pigeons/Analysis/PaleoMix_Re-Sequencing"
GBS="~/data/Pigeons/Analysis/PaleoMix_GBS"
Pairs="~/data/Pigeons/Analysis/Samtools_WGS-GBS"

for query in $SampleNames
do
    echo samtools index ${Pairs}/${query}-WGS-GBS.RockDove_DoveTail_ReRun.realigned.bam
    
done | xsbatch -c 1 -R --max-array-jobs 1 --mem-per-cpu 2024 -J Index --time 1-00 --

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