How to extract YSTR markers from WGS400 using Last and tandem-genotypes

last_YSTR_hg38_pipeline.sh

#!/bin/bash
START=$(date +%s.%N)
clear
# setup parameters

YSEQID=${PWD##*/}
# YSEQID="1234" # (the above command simply gets the name of the last segment of the current working directory)

NUM_THREADS=$(getconf _NPROCESSORS_ONLN)
echo "We can use ${NUM_THREADS} threads."


# Whole genome
# REF="/genomes/0/refseq/hg38/last/hg38.fa"
# REFDB="/genomes/0/refseq/hg38/last/mydb"

# ChrY only
REF="/genomes/0/refseq/hg38/last/hg38_chrY.fa"
REFDB="/genomes/0/refseq/hg38/last/chrYdb"

# If the reference is not yet indexed, we need to index it with lastdb:
# lastdb -P ${NUM_THREADS} -uNEAR ${REFDB} ${REF}



REFPAR="${YSEQID}_last.par"

# YSTR_hg38.bed is available here below vv
MICROSAT="/genomes/0/refseq/hg38/last/YSTR_hg38.bed"
CHRY_BAMFILE_INPUT="/genomes/arch/${YSEQID}/${YSEQID}_bwa-mem_hg38_chrY.bam"

READS="${YSEQID}_chrY_reads.fasta"

# Extract just the chrY reads in fasta format
samtools fasta ${CHRY_BAMFILE_INPUT} >${READS}

# separate a few training reads
head -n 100000 ${READS} >training_reads.fa

MAF="${YSEQID}_last_hg38.maf"
SAMFILE="${YSEQID}_last_hg38.sam"
BAMFILE="${YSEQID}_last_hg38.bam"
BAMFILE_SORTED="${YSEQID}_last_hg38_sorted.bam"
TANDEM_GENOTYPES="${YSEQID}_tandem_genotypes.tsv"

# Last DNA-DNA mapping software is available here:
# https://gitlab.com/mcfrith/last

# Train the substitution and gap rates (if necessary)
last-train -P${NUM_THREADS} -Q0 ${REFDB} training_reads.fa > ${REFPAR}
rm -f training_reads.fa

# Pipeline commands:
lastal -P${NUM_THREADS} -p ${REFPAR} ${REFDB} ${READS} | \
        last-split -fMAF > ${MAF}
        

# Tandem-Genotypes is available here:
# https://github.com/mcfrith/tandem-genotypes

# Run Tandem-Genotypes 

tandem-genotypes -f 7 ${MICROSAT} ${MAF} > ${TANDEM_GENOTYPES}
tandem-genotypes-plot -c6 -r21 ${TANDEM_GENOTYPES}

END=$(date +%s.%N)

DIFF=$(echo "$END - $START" | bc)
echo ${DIFF}

YSTR_hg38.bed

chrY	24005952	24006099	CCTT	CDY	36
chrY	3284190	3284260	TATTT	DXYS156	12
chrY	18278507	18278547	AAC	DYF395	15
chrY	22022402	22022434	AAT	DYF397	11
chrY	22950279	22950378	AAAG	DYF399	24
chrY	23739648	23739707	GAAA	DYF401	15
chrY	21681709	21681748	TATC	DYF406S1	10
chrY	17912087	17912121	ATAG	DYF408	8
chrY	18486683	18486740	AAAGG	DYF411	11
chrY	20731419	20731492	CTTT	DYR1	17
chrY	17388715	17388774	GAAA	DYR33	15
chrY	12080037	12080096	TAGA	DYR76	15
chrY	19302303	19302351	GAAA	DYR112	12
chrY	11963243	11963291	ATAG	DYR150	12
chrY	15211391	15211447	GAAG	DYR157	14
chrY	9684380	9684443	TATC	DYS19	15
chrY	18680632	18680687	GAAA	DYS385	11
chrY	12635604	12635639	AAT	DYS388	12
chrY	12500564	12500611	GATA	DYS389B	16
chrY	12500448	12500516	GATA	DYS389B.2	12
chrY	12500449	12500495	GATA	DYS389I	12
chrY	15163067	15163162	TAGA	DYS390	24
chrY	11982089	11982132	TCTA	DYS391	11
chrY	20471987	20472025	AAT	DYS392	13
chrY	3263111	3263158	AGAT	DYS393	12
chrY	13987208	13987253	TG	DYS413	23
chrY	18041622	18041651	TGT	DYS425	10
chrY	17022970	17023005	TGT	DYS426	12
chrY	12345806	12345841	ATCT	DYS434	9
chrY	12384503	12384538	TGGA	DYS435	11
chrY	13091948	13091983	AAC	DYS436	12
chrY	12346267	12346326	TCTA	DYS437	15
chrY	12825899	12825948	CTTTT	DYS438	12
chrY	12403517	12403566	AGAT	DYS439	12
chrY	12869907	12869966	TTCC	DYS441	13
chrY	12649172	12649237	GATA	DYS442	12
chrY	17114312	17114367	ATAG	DYS444	13
chrY	19930716	19930763	TTTA	DYS445	12
chrY	3263417	3263486	TCTCT	DYS446	14
chrY	13166829	13166953	TATAT	DYS447	23
chrY	22218924	22219078	AGAGAT	DYS448	19
chrY	8349973	8350138	TTTC	DYS449	30
chrY	8258259	8258303	TTTTA	DYS450	8
chrY	19458592	19458746	TACTA	DYS452	31
chrY	8356115	8356158	AAAT	DYS454	11
chrY	7043528	7043571	AAAT	DYS455	11
chrY	4402919	4402978	AGAT	DYS456	15
chrY	7999839	7999902	GAAA	DYS458	16
chrY	23932704	23932743	TTAT	DYS459	10
chrY	18888956	18888995	TATC	DYS460	10
chrY	18888804	18888851	TATC	DYS461	12
chrY	19155161	19155204	TACA	DYS462	11
chrY	7775468	7775587	GAAAG	DYS463	24
chrY	24941464	24941523	CCTT	DYS464	15
chrY	12500662	12500716	GATA	DYS467	14
chrY	14396604	14396627	TAA	DYS472	8
chrY	8558337	8558402	CTT	DYS481	22
chrY	19937748	19937795	TTA	DYS485	15
chrY	9046133	9046171	TTA	DYS487	13
chrY	3575724	3575759	TTA	DYS490	12
chrY	15302457	15302489	ATT	DYS492	12
chrY	19224282	19224311	TTA	DYS494	10
chrY	12899385	12899434	ATT	DYS495	16
chrY	16053588	16053629	TTA	DYS497	14
chrY	3035192	3035263	TCCT	DYS504	18
chrY	3772790	3772837	TCCT	DYS505	12
chrY	15188019	15188083	TAGA	DYS510	17
chrY	15193041	15193080	ATAG	DYS511	9
chrY	15329904	15329951	TATC	DYS513	12
chrY	15208001	15208217	AAGA	DYS518	38
chrY	7862381	7862470	GATA	DYS520	19
chrY	7547584	7547623	GATA	DYS522	10
chrY	7208814	7208853	TAGA	DYS525	10
chrY	8598154	8598197	AAAT	DYS531	11
chrY	8511105	8511164	TTCT	DYS532	15
chrY	16281346	16281393	ATCT	DYS533	12
chrY	16281096	16281155	CTTT	DYS534	15
chrY	17246970	17247009	TCTA	DYS537	10
chrY	16453355	16453402	TTAT	DYS540	12
chrY	19358338	19358389	GATA	DYS549	13
chrY	11981555	11981692	TCTA	DYS552	24
chrY	20439567	20439610	AATA	DYS556	11
chrY	21072786	21072889	TTTC	DYS557	16
chrY	14452471	14452514	GATA	DYS561	15
chrY	14414852	14414895	ATAA	DYS565	12
chrY	8954511	8954554	AAAT	DYS568	11
chrY	6993190	6993257	TTTC	DYS570	17
chrY	3811619	3811658	AAAT	DYS572	10
chrY	7568216	7568255	AAAT	DYS575	10
chrY	7185318	7185385	AAAG	DYS576	17
chrY	20400678	20400713	AAAT	DYS578	9
chrY	15916825	15916915	ATACA	DYS587	18
chrY	22339546	22339610	TTATT	DYS589	12
chrY	8687939	8687978	TTTTG	DYS590	8
chrY	16473882	16473956	AAAAC	DYS593	15
chrY	19494951	19495000	AAATA	DYS594	10
chrY	16302502	16302577	GAAG	DYS607	15
chrY	8633472	8633762	CTT	DYS614	18
chrY	16969638	16969673	TTA	DYS617	12
chrY	22270860	22270932	AAAG	DYS626	27
chrY	13797171	13797206	CATT	DYS632	9
chrY	12258860	12258951	ATAG	DYS635	23
chrY	20472971	20473014	TTTA	DYS636	12
chrY	15533611	15533654	ATTT	DYS638	11
chrY	3411661	3411696	AAAT	DYS640	11
chrY	14022416	14022455	TAAA	DYS641	10
chrY	15314132	15314186	CTTTT	DYS643	11
chrY	15669604	15669694	TTTTA	DYS644	16
chrY	10015306	10015373	AAGG	DYS650	18
chrY	56887113	56887142	GTT	DYS655	10
chrY	7849529	7849775	CTTTC	DYS684	57
chrY	17324793	17324930	AAAG	DYS710	34.2
chrY	8465426	8465675	CTT	DYS711	64
chrY	13446553	13446620	AGAT	DYS712	22
chrY	7964032	7964245	TCTT	DYS713	42
chrY	19985845	19985979	TTTCT	DYS714	27
chrY	15550275	15550423	ATGG	DYS715	26
chrY	10629615	10629699	CTCCA	DYS716	27
chrY	15201365	15201444	TGTAT	DYS717	20
chrY	15170062	15170137	GATA	DYS723	20
chrY	23104466	23104537	GT	DYS725	32
chrY	11446663	11446765	AAGG	DYS726	12
chrY	11910967	11911130	TTTC	DYS727	13
chrY	18642119	18642156	TG	DYS728	19
chrY	16606999	16607058	TATC	Y-GATA-A10	13
chrY	16631673	16631720	TCTA	Y-GATA-H4	12
chrY	10687563	10687627	TTCCA	Y-GGAAT-1B07	10
chrY	17510231	17510276	CA	YCAII	23