Fragmented

1. chr1: 154930735 (50bp insertion)

On the HPRC assemblies, it's broken into two events brecause the insertion is smaller on one haplotype.  But on your contigs, the insertion is the same size in both haplotypes.

HPRC-GRAPH:

chr1	154930718	>5548040>5548032	A	AATAACATAACATAACATAAC	60	.	AC=1;AF=0.258427;AN=2;AT=>5548040>554803
2,>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=>554803
2>5548027,>5548032>5548031>5548029>5548028>5548027;NS=45;LV=0	GT	1|1

CONTIGS-GRAPH:

chr1	154930734	>1125686>1125688	C	CATAACATAACATAACATAACATAACATAAT	60	.	AC=2;AF=1;AN=2;AT=>1125686>1125688,>1125686>1125687>1125688;NS=1;LV=0	GT	1|1


2. chr1: 53166143 (140bp insertion)

There's an insertion in every graph, but shifted around.

HPRC:

chr1	53165358	>976403>976405	T	TACATACCCGGGCCACTTACTTACCTACTACACACCCGGGCCGCTTACTTACCTACTACACACCCGGGCCGCTTACTTACCTACTACACACCCGGGCCGCTTACTTACCTACTACACACCCGGGCCGCTTACTTACCTACTACACACCCGGGCCGCTTACTTACCTACTACACACCCGGGCCGCTTACTTACCTACTACACACCCGGGCCGCTTACTTACCTACTACACACCCGGGCCGCTTACTTACCTACTACATACCCGGGCCGCTTACTTACCTACTACATACCCGGGCCGCTTACTTACCTACTACATACCCGGGCCGCTTACTTACC

CONTIGS:

chr1	53166031	>678079>678081	A	ACATACCCGGGCCGCTTACTTACCTACTACATACCCGGGCCGCTTACTTACCTACTACATACCCGGGCCGCTTACTTACCTACTACATACCCGGGCCGCTTACTTACCTACTACATACCCGGGCCGCTTACTTACCTACTACATACCCGGGCCGCTTACTTACCTACTACATACCCGGGCCGCTTACTTACCTACTACATACCCGGGCCGCTTACTTACCTACTACATACCCGGGCCGCTTACTTACCTACTACATACCCGGGCCGCTTACTTACCTACTACATACCCGGGCCGCTTACTTACCTACTACATACCCGGGCCGCTTACTTACCTACTACATACCCGGGCCGCTTACTTACCTACTG	60	.	AC=1;AF=0.5;AN=2;AT=>678079>678081,>678079>678080>678081;NS=1;LV=0	GT	0|1


3. chr1: 2109087 (Missing 1164 bp deletion)

The only graph that gets this one is the HG00438-only graph with the HPRC assemblies. Very strong candidate of graph-building bug. 

4. chr1: 245901000 (Missing 188 (or 94?) bp deletion - have 47bp deletion instead)

There are three deletions around here in every graph.  The HPRC-assembly based deletions are more fragmented than the contig-based deletions.

Missing

5. chr1: 144642608 (Missing 62bp insertion)

This appears in no HPRC-assembly-based graphs, but does in the contig-based graph

chr1	144642607	>652214>652216	A	ATATATATACATACACATTGTGTGTATGTATATATATATATATACATACACATTGTGTGTATG	60	.	AC=1;AF=1;AN=1;AT=>652214>652216,>652214>652215>652216;NS=1;LV=0	GT	.|1


6. chr1: 223201981 (Missing 1267 bp insertion)

This one appears in both HG00438-only graphs, but not the full HPRC graph. Probably graph-building bug.

7. chr1: 135590901 (Missing 2165 bp deletion)

Region completely missing from graph -- listed as HSAT in browser. 


export HPRCVCF=chr1.dec.vcf.gz
export NEWVCF=hprc-new-jan18-mc-chm13-hg00438.norm.vcf.gz
export OLDVCF=hprc-v1.1-mc-chm13-hg00438.norm.vcf.gz

bcftools view -H ${HPRCVCF} -r chr1:154929735-154931735 > case_1h.vcf
bcftools view -H ${NEWVCF} -r chr1:154929735-154931735 > case_1n.vcf
bcftools view -H ${OLDVCF} -r chr1:154929735-154931735 > case_1o.vcf

bcftools view -H ${HPRCVCF} -r chr1:53165143-53167143 > case_2h.vcf
bcftools view -H ${NEWVCF} -r chr1:53165143-53167143 > case_2n.vcf
bcftools view -H ${OLDVCF} -r chr1:53165143-53167143 > case_2o.vcf

bcftools view -H ${HPRCVCF} -r chr1:2108087-2110087 > case_3h.vcf
bcftools view -H ${NEWVCF} -r chr1:2108087-2110087 > case_3n.vcf
bcftools view -H ${OLDVCF} -r chr1:2108087-2110087 > case_3o.vcf

bcftools view -H ${HPRCVCF} -r chr1:245900000-245903000 > case_4h.vcf
bcftools view -H ${NEWVCF} -r chr1:245900000-245903000 > case_4n.vcf
bcftools view -H ${OLDVCF} -r chr1:245900000-245903000 > case_4o.vcf

bcftools view -H ${HPRCVCF} -r chr1:144641608-144643608 > case_5h.vcf
bcftools view -H ${NEWVCF} -r chr1:144641608-144643608 > case_5n.vcf
bcftools view -H ${OLDVCF} -r chr1:144641608-144643608 > case_5o.vcf

bcftools view -H ${HPRCVCF} -r chr1:223200981-223202981 > case_6h.vcf
bcftools view -H ${NEWVCF} -r chr1:223200981-223202981 > case_6n.vcf
bcftools view -H ${OLDVCF} -r chr1:223200981-223202981 > case_6o.vcf

bcftools view -H ${HPRCVCF} -r chr1:135587901-135593901 > case_7h.vcf
bcftools view -H ${NEWVCF} -r chr1:135587901-135593901 > case_7n.vcf
bcftools view -H ${OLDVCF} -r chr1:135587901-135593901 > case_7o.vcf