Overview
    Assessment 1
        -sim_1_t10_PacBio_SVs_clean/
        -sim_2_t10_ONTech_SVs_clean/
    Assessment 2
        -Ashkenazim_trio_clean/


Assessment 1 Simulated SVs
    Simulated PacBio long-read SVs assessment dataset
    The dataset simulated SVs of different types and size embedded in long reads of different sequencing error.
    It is to assess if aligners will forcibly align SVs embedded in long reads.

    sim_1_t10_PacBio_SVs_clean/
    |-- del
    |   |-- chr1_80_10000_0001.fastq
    |   |-- chr1_80_10000_0001.maf
    |   |-- del+80_1000.fa
    |   |__ del+80_1000.list
    |-- dup
    |-- ins
    |__ inv

    - f1.chr1_80_10000_0001.fastq
        Long reads whose sequencing error on average = 1-0.8 and length on average = 10000bps.
        The reads are simulated from chromosome 1.
    - f2.chr1_80_10000_0001.maf
        Exact positions of the genome where the reads in f1 are simulated.
    - f3.del+80_1000.fa
        Long reads in f1 embedded with deletions (dels) of length 1000bps.
    - f4.del+80_1000.list
        Endpoints of the dels in f3:
            col1 col2 col3 col4
            S1_1 2453 2653 200
        col1 : Read id
        col2 : The SV starts here in the read
        col3 : The Sv ends here in the read
        col4 : The length of SVs


    Results
        File name format: <Tool>_<SV>+<seqErr>_<SV Length>.fa.sam
        [1] Linear_del+80_1000.fa.sam ...
        [2] Minimap2_del+80_1000.fa.sam ...
        [3] NGMLR_del+80_1000.fa.sam ...

        minimap2 <chr1.fa> <reads> -t 10 -a -x map-pb
        ngmlr -r <chr1.fa> -q <reads> -x pacbio -t 10
        linear <reads> x <chr1.fa> -t 10 -o all -dup 1 #for dup/
        linear <reads> x <chr1.fa> -t 10 -o all
        Compare .sam to corresponding .list (f4) to count forced alignment of SVs.

    sim_1_t10_ONTech_SVs_clean/ is organised in the same way.
    Except the following files of simulated reads use different file name 
        |-- normval+_75.fa
        |-- normval+_80.fa
        |-- normval+_85.fa
        |__ normval+_90.fa





Assessment 2 Real SVs
    Ashkenazim_trio_clean
    |__ HG002
        |-- data
        |     |-- ONTech
        |     |     |-- SRR18363747
        |     |     |-- SRR18363749
        |     |     |__ SRR18363750
        |     |-- PacBio_hifi_HG002_NA24385_son
        |     |     |-- deepvariant_HG002_GRCh38_15kb_20kb_53X_SequelII.vcf
        |     |     |-- download_list
        |     |     |-- download.sh
        |     |     |-- gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf
        |     |     |-- HG002_GRCh38_1_22_v4.2.1_benchmark.vcf
        |     |     |-- HG002_GRCh38_CMRG_smallvar_v1.00.vcf
        |     |     |-- HG002_GRCh38_CMRG_SV_v1.00.vcf
        |     |     |-- pbsv_HG003_SequelII.GRCh38.vcf
        |     |     |__ true_set_hg002_hifi_t3
        |     |__ PacBio_MtSinai_NIST
        |         |-- download.sh
        |         |-- README.txt
        |         |__ true_set_hg002_PacBio_MtSinai_NIST
        |-- linear
        |     |-- result_hg002_hifi_t3
        |     |     |-- all2_sort.bam
        |     |     |-- all2_sort.bam.bai
        |     |     |__ cuteSV
        |     |         |-- cute.vcf
        |     |         |-- false_positives
        |     |         |__ true_positives
        |     |-- result_nano
        |     |     |__ cuteSV
        |     |         |__ cute.vcf
        |     |__ result_PacBio_MtSinai_NIST
        |         |-- all2_sort.bam.bai
        |         |-- all3_sort.bam.bai
        |         |-- cuteSV
        |         |     |-- cute.vcf
        |         |     |-- false_positives
        |         |     |__ true_positives
        |         |__ pbsv
        |             |-- DEL_10_103394012_103395092_-1080.bam
        |             |-- DEL_10_103394012_103395092_-1080.vcf
        |             |__ DEL_10_107252998_107253351_-353.bam
        |-- minimap2
        |     |-- result_hg002_hifi_t3
        |     |     |-- all.bam.bai
        |     |     |__ cuteSV
        |     |         |-- cute.vcf
        |     |         |-- false_positives
        |     |         |__ true_positives
        |     |__ result_PacBio_MtSinai_NIST
        |         |-- all2_sort.bam.bai
        |         |__ cuteSV
        |             |-- cute.vcf
        |             |-- false_positives
        |             |__ true_positives
        |__ sksv
            |__ result_hg002_hifi_t3
                |-- false_positives
                |-- sksv.vcf
                |__ true_positive   

    - d1.   data/ 
                [1] Reads(.fa) to run the assessment (Large files not shown)
                [2] SVs(.vcf) from GIAB project
                [3] SVs as the ground truth (true*)

    - d12.  data/PacBio_hifi_HG002_NA24385_son
                PacBio HiFi reads from GIAB.
                Use download.sh with download.list to download all the reads (.fa) for the assessment
    - d2.   linear/
                Results of all tests for Linear
                Large files such as .bam are probably not presented due to the size limitation of the server
    - d21.  linear/result_hg002_hifi_t3
                Results on hg002_hifi_t3.
                Corresponding reads, SVs ground truth are in d1/PacBio_hifi_HG002_NA24385_son
    - d211. linear/result_hg002_hifi_t3/cuteSV
                Results of Linear-cuteSV:
                [1] cute.vcf : detected SVs
                [2] false_positives : false positive SVs of Linear-cuteSV
                [3] true_positives :  true positive SVs of Linear-cuteSV
                    col1 col2   col3       col4 col5 col6
                    chr1 629085 sv_len=182 BND 308 3.08e-17
                    ...
                col1:Reference genome
                col2:Position of the SVs in the reference genome
                col3:SV lengths
                col4:SV types
                col5:Supported reads
                col6:Temporary

    - d232. linear/result_PacBio_MtSinai_NIST/pbsv 
                Resutls of Linear-PBSV on the high-quality SV callset:
                File name format: <Type>_<Genome>+<Start>_<End>_<Length>
                [1]DEL_10_103394012_103395092_-1080.bam
                [2]DEL_10_103394012_103395092_-1080.vcf
                Results of DEL of 1080bps starting from 103394012bps to 103395092bps chromosome 10

    Results

        minimap2  -a -x map-pb <ref> <reads>
        SKSV-skeleton index <ref> <index>
        SKSV-skeleton aln <index> <reads>
        linear <reads> <ref>

        samtools sort  <sam> <bam>
        samtools index <bam>

        cuteSV --genotype 1 <bam> <ref> cute.vcf

        Filter SVs > 100bps, Support=10 in cute.vcf for PacBio_MtSinai_NIST raw reads
        Filter SVs > 100bps, Support=20 in cute.vcf for PacBio_hifi_HG002_NA24385_son hifi reads
        Compare filtered SVs to true_set* in data/* (d12) to get the true_positives and false_positives

        pbsv discover <bam> <output.svsig.gz>
        pbsv call -t [INS/DEL] <reference> <output.svsig.vcf> <output.vcf>



Notation
    [1]  We limit *bam, *sam *fa(stq) and other very large files due to the disk size limitation of the web server.