Role of haplotype map in CrosscheckFingerprint when no ANCHOR_SNPs are defined

[harrymatthews50]

I have the job of assessing a pipeline (not implemented by me) for correctness. It is for somatic variant calling with paired tumour-normal samples. As part of the pipeline CrosscheckFingerprint is run comparing the tumour to normal. It is given a custom haploytype map that has no entries in the ANCHOR_SNP columnI .e. the haplotype map is not actually defining any haplotypes. What does CrosscheckFingerprint do with this information in this case (if anything)?

#CHROMOSOME POSITION    NAME    MAJOR_ALLELE    MINOR_ALLELE    MAF ANCHOR_SNP  PANELS
chr1	4071665	rs3936238	C	T	0.3			
chr1	11130588	rs2275527	C	T	0.3			
chr1	11145000	rs1057079	A	G	0.3			
chr1	11241656	rs1135172	C	T	0.3			
chr1	11429620	rs877309	A	G	0.3			
chr1	21325683	rs213028	C	T	0.3			
chr1	24951490	rs11249206	C	T	0.3			
chr1	81707362	rs654498	C	T	0.3			
chr1	109757818	rs3818562	C	T	0.3			
chr1	177462031	rs715359	A	G	0.3			
chr1	181362696	rs2804694	C	T	0.3			
chr1	204455899	rs3765156	A	G	0.3			
chr1	245926508	rs6426327	A	G	0.3			
chr10	14649889	rs10796216	A	G	0.3			
chr10	96879339	rs10882854	C	T	0.3			
chr11	534241	rs12628	C	T	0.3			
chr11	38767064	rs11034952	C	T	0.3			
chr11	64805129	rs2071313	C	T	0.3			
chr11	69648141	rs9344	A	G	0.3			
chr11	105428996	rs1945975	C	T	0.3			
chr12	15863173	rs10846239	C	T	0.3			
chr12	42804919	rs2468330	C	T	0.3			
chr12	49032194	rs3741622	C	T	0.3			
chr12	63104355	rs1495031	C	T	0.3			
chr12	109670257	rs10774834	C	T	0.3			
chr12	132643244	rs5744944	A	G	0.3			
chr15	45707624	rs951295	A	G	0.3			
chr15	76121187	rs2959823	C	T	0.3			
chr16	56066611	rs1510189	A	G	0.3			
chr16	70269676	rs2070203	C	T	0.3			
chr17	73201608	rs1037256	A	G	0.3			
chr18	37582874	rs1941955	C	T	0.3			
chr19	3119240	rs4900	C	T	0.3			
chr19	10994931	rs7935	C	T	0.3			
chr19	42294896	rs1052023	C	T	0.3			
chr2	12008093	rs966367	C	T	0.3			
chr2	48857533	rs4331560	A	G	0.3			
chr2	60598305	rs1510480	A	G	0.3			
chr2	69033224	rs6546473	A	G	0.3			
chr2	159114850	rs264581	C	T	0.3			
chr20	1989287	rs2235751	A	G	0.3			
chr20	58903751	rs7121	C	T	0.3			
chr21	32625973	rs845016	C	T	0.3			
chr21	37105029	rs2032088	A	G	0.3			
chr22	20983035	rs13054014	A	G	0.3			
chr22	25535404	rs1467387	C	T	0.3			
chr22	25748792	rs133860	C	T	0.3			
chr22	26960615	rs739259	A	G	0.3			
chr22	29659684	rs2857639	A	G	0.3			
chr22	47819062	rs2208123	A	G	0.3			
chr3	14617358	rs939290	C	T	0.3			
chr3	86613004	rs9839873	C	T	0.3			
chr3	99254081	rs1520670	C	T	0.3			
chr3	161184742	rs10936224	A	G	0.3			
chr4	14355505	rs10033147	A	G	0.3			
chr4	127686676	rs2125573	A	G	0.3			
chr4	130122894	rs7660805	A	G	0.3			
chr4	137116127	rs10155413	C	T	0.3			
chr5	35000206	rs9292570	C	T	0.3			
chr5	113489979	rs348937	A	G	0.3			
chr5	147268795	rs1019916	A	G	0.3			
chr6	33320493	rs1059231	C	T	0.3			
chr6	47163082	rs7746156	C	T	0.3			
chr6	67522148	rs9363764	A	G	0.3			
chr6	148721663	rs10457834	C	T	0.3			
chr8	36689794	rs6982811	C	T	0.3			
chr8	50813093	rs1484127	A	G	0.3			
chr8	95458071	rs6471533	A	G	0.3			
chr8	95836515	rs472920	C	T	0.3			
chr8	120770161	rs6991394	C	T	0.3			
chr8	125669751	rs2385226	C	T	0.3			
chr9	7711757	rs4742386	A	G	0.3			
chr9	82800621	rs1040870	C	T	0.3			
chr9	118597413	rs1414097	C	T	0.3			
chr9	136503254	rs10521	A	G	0.3			
chr9	136513479	rs2229971	C	T	0.3			
chrX	9508949	rs2521373	C	T	0.3			
chrX	15867307	rs798149	A	G	0.3			
chrX	28229213	rs5926356	A	G	0.3			
chrX	69846980	rs5936512	A	G	0.3			
chrX	115476350	rs5987737	C	T	0.3			
chrX	137995697	rs5931272	A	G	0.3			
chrX	146137646	rs1416770	C	T	0.3			
chrX	148122852	rs6626309	C	T	0.3