Hi,
I am running the ont-spectre v0.3.2
I have done the initial single sample calls and get results as expected.
When I run spectre population providing the intermediate files I seem to get the calls listed under the wrong samples. It appears that the sample names are as provided however the entires are in the wrong columns. The columns always seem to provide alphabetical order regardless of input order. If I change the order of the intermediate files to be in alphabetical order I get expected results.
spectre population \
--candidates LR-115_father-F139924.spc.gz LR-115_mother-F139923.spc.gz LR-115_proband-F139921.spc.gz \
--sample-id LR-115 \
--output-dir spectre_output2/ \
--reference hg38_no_alt.fa
gives expected results with expected proband (third column) alteration under proband in third column.
spectre population \
--candidates LR-115_father-F139924.spc.gz LR-115_proband-F139921.spc.gz LR-115_mother-F139923.spc.gz \
--sample-id LR-115 \
--output-dir spectre_output/ \
--reference hg38_no_alt.fa
puts the expected proband (second column) alteration under mother in third column.
spectre population \
--candidates LR-115_proband-F139921.spc.gz LR-115_father-F139924.spc.gz LR-115_mother-F139923.spc.gz \
--sample-id LR-115 \
--output-dir spectre_output3/ \
--reference hg38_no_alt.fa
puts the expected proband (first column) alteration under mother in third column
we can see here the expected call is always in the third position regardless of the order provided and the sample column names.
(base) [dmulder@nextflow01 36b75dfe28818bee712d9dff25e3c3]$ for f in spectre_output*; do echo $f; cat $f/LR-115_spectre_cnv_joint.vcf | grep -v "^##" | grep "^#"; grep 2232000 $f/LR-115_spectre_cnv_joint.vcf; done
spectre_output
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT LR-115_father-F139924 LR-115_proband-F139921 LR-115_mother-F139923
chr7 2232000 Spectre.DEL.WRJYN5QL N <DEL> . . END=2533000;SVLEN=301000;SVTYPE=DEL;CN=1;SUPP_VEC=001 GT:HO:GQ:CN:ID ./.:0.0:0:NULL ./.:0.0:0:NULL 0/1:0.0:60:Spectre.DEL.WRJYN5QL
spectre_output2
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT LR-115_father-F139924 LR-115_mother-F139923 LR-115_proband-F139921
chr7 2232000 Spectre.DEL.WRJYN5QL N <DEL> . . END=2533000;SVLEN=301000;SVTYPE=DEL;CN=1;SUPP_VEC=001 GT:HO:GQ:CN:ID ./.:0.0:0:NULL ./.:0.0:0:NULL 0/1:0.0:60:Spectre.DEL.WRJYN5QL
spectre_output3
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT LR-115_proband-F139921 LR-115_father-F139924 LR-115_mother-F139923
chr7 2232000 Spectre.DEL.WRJYN5QL N <DEL> . . END=2533000;SVLEN=301000;SVTYPE=DEL;CN=1;SUPP_VEC=001 GT:HO:GQ:CN:ID ./.:0.0:0:NULL ./.:0.0:0:NULL 0/1:0.0:60:Spectre.DEL.WRJYN5QL
Hi,
I am running the ont-spectre v0.3.2
I have done the initial single sample calls and get results as expected.
When I run spectre population providing the intermediate files I seem to get the calls listed under the wrong samples. It appears that the sample names are as provided however the entires are in the wrong columns. The columns always seem to provide alphabetical order regardless of input order. If I change the order of the intermediate files to be in alphabetical order I get expected results.
gives expected results with expected proband (third column) alteration under proband in third column.
puts the expected proband (second column) alteration under mother in third column.
puts the expected proband (first column) alteration under mother in third column
we can see here the expected call is always in the third position regardless of the order provided and the sample column names.