tkrahn/YSTR_hg38.bed

## 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
	#!/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}
	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