Hello,
I'd like to know if you have implemented or will implement an option to force the ploidy per chromosome ? Especially gonosomes.
Since patients are often grafted with bone marrow from the opposite sex, it would be very nice to force an expected ploidy, to better call on a small population of cells.
Also, when plotting a XY sample, even if the bam is tagged, wakhan still interpret the data from chrY as coming from different haplotypes :
The bam is simulated, that's why the chrX is absent. You can also see that it incorrectly calls two duplication on this chrX.
Second, i also simulated in this bam an almost complete heterozygous deletion of the chr5 :
chr5 14624519 nssv15755807 C . . END=149511942;SVLEN=-134826806;SVTYPE=DEL
GT 1|0
chr5 162131840 nssv17682161 A . . END=172600001;SVLEN=-11570002;SVTYPE=DEL
GT 1|0
But wakhan is calling an homozygous deletion :
chr5 14624518 wakhan:LOSS:chr5:14624518-46000000 N 1000 PASS SVTYPE=CNV;SVLEN=31375482;END=46000000;BPS= GT:TCN:CN1:CN2:CNQ1:CNQ2:COV1:COV2 1/1:0.0:0.0:0.0:0.9464838:0.9491931:1.11:2.07
chr5 46000001 wakhan:LOSS:chr5:46000001-52000000 N 1000 PASS SVTYPE=CNV;SVLEN=5999999;END=52000000;BPS= GT:TCN:CN1:CN2:CNQ1:CNQ2:COV1:COV2 1/1:0.0:0.0:0.0:0.9510576:0.9318339:1.18:2.29
chr5 52000001 wakhan:LOSS:chr5:52000001-82623594 N 1000 PASS SVTYPE=CNV;SVLEN=30623593;END=82623594;BPS=severus_BND1611_2,severus_BND1637_2,severus_BND1637_1,severus_BND1611_1 GT:TCN:CN1:CN2:CNQ1:CNQ2:COV1:COV2 1/1:0.0:0.0:0.0:0.9574477:0.9656901:1.23:1.86
chr5 82623595 wakhan:LOSS:chr5:82623595-149511942 N 1000 PASS SVTYPE=CNV;SVLEN=66888347;END=149511942;BPS=severus_BND2102_1,severus_BND2102_2 GT:TCN:CN1:CN2:CNQ1:CNQ2:COV1:COV2 1/1:0.0:0.0:0.0:0.9511889:0.9593289:1.15:1.94
chr5 162131840 wakhan:LOSS:chr5:162131840-172600001 N 1000 PASS SVTYPE=CNV;SVLEN=10468161;END=172600001;BPS=severus_BND2139_1,severus_BND2139_2 GT:TCN:CN1:CN2:CNQ1:CNQ2:COV1:COV2 1/1:0.0:0.0:0.0:0.9783196:0.9940934:1.49:1.51
Since the data are simulated, i'm sure that the HP tag is set on all reads and consistant. Is there a way to completed the calling with the HP tag from the bam maybe ?
Thank you for your time
Hello,
I'd like to know if you have implemented or will implement an option to force the ploidy per chromosome ? Especially gonosomes.
Since patients are often grafted with bone marrow from the opposite sex, it would be very nice to force an expected ploidy, to better call on a small population of cells.
Also, when plotting a XY sample, even if the bam is tagged, wakhan still interpret the data from chrY as coming from different haplotypes :
The bam is simulated, that's why the chrX is absent. You can also see that it incorrectly calls two duplication on this chrX.
Second, i also simulated in this bam an almost complete heterozygous deletion of the chr5 :
chr5 14624519 nssv15755807 C
. . END=149511942;SVLEN=-134826806;SVTYPE=DELGT 1|0
chr5 162131840 nssv17682161 A
. . END=172600001;SVLEN=-11570002;SVTYPE=DELGT 1|0
But wakhan is calling an homozygous deletion :
chr5 14624518 wakhan:LOSS:chr5:14624518-46000000 N
1000 PASS SVTYPE=CNV;SVLEN=31375482;END=46000000;BPS= GT:TCN:CN1:CN2:CNQ1:CNQ2:COV1:COV2 1/1:0.0:0.0:0.0:0.9464838:0.9491931:1.11:2.07chr5 46000001 wakhan:LOSS:chr5:46000001-52000000 N
1000 PASS SVTYPE=CNV;SVLEN=5999999;END=52000000;BPS= GT:TCN:CN1:CN2:CNQ1:CNQ2:COV1:COV2 1/1:0.0:0.0:0.0:0.9510576:0.9318339:1.18:2.29chr5 52000001 wakhan:LOSS:chr5:52000001-82623594 N
1000 PASS SVTYPE=CNV;SVLEN=30623593;END=82623594;BPS=severus_BND1611_2,severus_BND1637_2,severus_BND1637_1,severus_BND1611_1 GT:TCN:CN1:CN2:CNQ1:CNQ2:COV1:COV2 1/1:0.0:0.0:0.0:0.9574477:0.9656901:1.23:1.86chr5 82623595 wakhan:LOSS:chr5:82623595-149511942 N
1000 PASS SVTYPE=CNV;SVLEN=66888347;END=149511942;BPS=severus_BND2102_1,severus_BND2102_2 GT:TCN:CN1:CN2:CNQ1:CNQ2:COV1:COV2 1/1:0.0:0.0:0.0:0.9511889:0.9593289:1.15:1.94chr5 162131840 wakhan:LOSS:chr5:162131840-172600001 N
1000 PASS SVTYPE=CNV;SVLEN=10468161;END=172600001;BPS=severus_BND2139_1,severus_BND2139_2 GT:TCN:CN1:CN2:CNQ1:CNQ2:COV1:COV2 1/1:0.0:0.0:0.0:0.9783196:0.9940934:1.49:1.51Since the data are simulated, i'm sure that the HP tag is set on all reads and consistant. Is there a way to completed the calling with the HP tag from the bam maybe ?
Thank you for your time