bcftools view hprc-v1.1-mc-chm13.vcfbub.a100k.wave.vcf.gz -r chr1 -s HG00438 | bcftools norm -f chm13.fa.gz | bcftools sort | grep -v "0|0" | bgzip  > chr1.dec.vcf.gz
tabix -fp vcf chr1.dec.vcf.gz

bcftools view hprc-v1.1-mc-chm13.raw.vcf.gz -r chr1 -s HG00438 -a | bcftools norm -f chm13.fa.gz | bcftools sort | grep -v "0|0" | bgzip  > chr1.raw.vcf.gz
tabix -fp vcf chr1.raw.vcf.gz


1) looks like 63bp insertion fragmented into smaller events

bcftools view  hprc-v1.1-mc-chm13.raw.vcf.gz -r chr1:210000000-220000000 | bcftools norm -f chm13.fa.gz | bcftools view -t chr1:214333670-214333790  -H -s HG00438 -a | grep -v "0|0"
Lines   total/split/realigned/skipped:	75975/0/3371/0
chr1	214333689	>3614552>3614567	A	ATATATAATATATAATATAAAAATATATTATATAT	60	.	AC=1;AF=0.337079;AN=2;AT=>3614552>3614567,>3614552>3614553>3614554>3614556>3614558>3614559>3614561>3614563>3614564>3614566>3614567;NS=45;LV=0	GT	1|0
chr1	214333701	>3614567>3614570	T	A	60	.	AC=1;AF=0.348315;AN=2;AT=>3614567>3614569>3614570,>3614567>3614568>3614570;NS=45;LV=0	GT	1|0
chr1	214333706	>3614570>3614572	TA	T	60	.	AC=1;AF=0.370787;AN=2;AT=>3614570>3614571>3614572,>3614570>3614572;NS=45;LV=0	GT	1|0
chr1	214333709	>3614572>3614576	AAATATATT	TT	60	.	AC=1;AF=0.348315;AN=2;AT=>3614572>3614573>3614574>3614575>3614576,>3614572>3614575>3614576;NS=45;LV=0	GT	1|0
chr1	214333729	>3614582>3614588	A	AATATATA	60	.	AC=1;AF=0.707865;AN=2;AT=>3614582>3614588,>3614582<3614583>3614586>3614587>3614588;NS=45;LV=0	GT	1|0
chr1	214333730	>3614579>3614582	A	T	60	.	AC=1;AF=0.741573;AN=2;AT=>3614579>3614581>3614582,>3614579>3614580>3614582;NS=45;LV=0	GT	1|0
chr1	214333735	>3614588>3614594	T	AAATATATTATATATTATATATTATATATAA	60	.	AC=1;AF=0.719101;AN=2;AT=>3614588>3614590>3614594,>3614588>3614589>3614591>3614593>3614594;NS=45;LV=0	GT	1|0


2) ??

3)

bcftools view chr1.raw.norm.vcf.gz -H chr1:154930535-154930935
chr1	154930543	>5548054>5548051	C	.	60	.	AN=2;AT=>5548054>5548052>5548051;NS=45;LV=0	GT	0|0
chr1	154930564	>5548051>5548048	A	G	60	.	AC=2;AF=0.303371;AN=2;AT=>5548051>5548049>5548048,>5548051<5548050>5548048;NS=45;LV=0	GT	1|1
chr1	154930694	>5548048>5548045	G	.	60	.	AN=2;AT=>5548048>5548046>5548045;NS=45;LV=0	GT	0|0
chr1	154930702	>5548045>5548042	T	C	60	.	AC=2;AF=0.921348;AN=2;AT=>5548045>5548044>5548042,>5548045>5548043>5548042;NS=45;LV=0	GT	1|1
chr1	154930715	>5548042>5548040	C	CA	60	.	AC=2;AF=0.898876;AN=2;AT=>5548042>5548040,>5548042>5548041>5548040;NS=45;LV=0	GT	1|1
chr1	154930718	>5548040>5548032	A	AATAACATAACATAACATAAC	60	.	AC=1;AF=0.258427;AN=2;AT=>5548040>5548032,>5548040<5548036>5548035>5548034>5548033>5548032;NS=45;LV=0	GT	1|0
chr1	154930719	>5548032>5548027	A	ATAACATAACATAACATAACATAAC	60	.	AC=2;AF=0.910112;AN=2;AT=>5548032>5548027,>5548032>5548031>5548029>5548028>5548027;NS=45;LV=0	GT	1|1
chr1	154930732	>5548027>5548024	A	.	60	.	AN=2;AT=>5548027>5548026>5548024;NS=45;LV=0	GT	0|0
chr1	154930734	>5548024>5548020	C	CATAAT	60	.	AC=2;AF=0.752809;AN=2;AT=>5548024>5548020,>5548024>5548023<5548022>5548020;NS=45;LV=0	GT	1|1


4)