hyunminkang
commented
6 years ago Not sure why it happens. Is the chromosome order in VCF header correct? Is it consistent to that of BAM?
Closed harmbrugge closed 5 years ago
hyunminkang
commented
6 years ago Not sure why it happens. Is the chromosome order in VCF header correct? Is it consistent to that of BAM?
harmbrugge
commented
6 years ago Yes I checked this thoroughly. The order of the header of the VCF file corresponds to ordering of the file and the BAM file is ordered in the same manner.
hyunminkang
commented
6 years ago If the order of chromosomes in VCF header also consistent with the order of chromosomes in the VCF records?
On Sat, Apr 7, 2018 at 5:06 PM Harm Brugge notifications@github.com wrote:
Yes I checked this thoroughly. The order of the header of the VCF file corresponds to ordering of the file and the BAM file is ordered in the same manner.
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hyunminkang
commented
6 years ago Sorry for the typo -- I mean to start with "Is", not "If"
On Mon, Apr 9, 2018 at 5:19 AM Hyun Min Kang hmkang@umich.edu wrote:
If the order of chromosomes in VCF header also consistent with the order of chromosomes in the VCF records?
On Sat, Apr 7, 2018 at 5:06 PM Harm Brugge notifications@github.com wrote:
Yes I checked this thoroughly. The order of the header of the VCF file corresponds to ordering of the file and the BAM file is ordered in the same manner.
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harmbrugge
commented
6 years ago Yes the header of the VCF file is consistent with the order of the records:
awk 'NR>17 {print $1}' sorted.vcf | uniq
##contig=<ID=1,length=249250621,assembly=b37>
##contig=<ID=10,length=135534747,assembly=b37>
##contig=<ID=11,length=135006516,assembly=b37>
##contig=<ID=12,length=133851895,assembly=b37>
##contig=<ID=13,length=115169878,assembly=b37>
##contig=<ID=14,length=107349540,assembly=b37>
##contig=<ID=15,length=102531392,assembly=b37>
##contig=<ID=16,length=90354753,assembly=b37>
##contig=<ID=17,length=81195210,assembly=b37>
##contig=<ID=18,length=78077248,assembly=b37>
##contig=<ID=19,length=59128983,assembly=b37>
##contig=<ID=2,length=243199373,assembly=b37>
##contig=<ID=20,length=63025520,assembly=b37>
##contig=<ID=21,length=48129895,assembly=b37>
##contig=<ID=22,length=51304566,assembly=b37>
##contig=<ID=3,length=198022430,assembly=b37>
##contig=<ID=4,length=191154276,assembly=b37>
##contig=<ID=5,length=180915260,assembly=b37>
##contig=<ID=6,length=171115067,assembly=b37>
##contig=<ID=7,length=159138663,assembly=b37>
##contig=<ID=8,length=146364022,assembly=b37>
##contig=<ID=9,length=141213431,assembly=b37>
##contig=<ID=X,length=155270560,assembly=b37>
##contig=<ID=Y,length=59373566,assembly=b37>
##contig=<ID=MT,length=16569,assembly=b37>
#CHROM
1
10
11
12
13
14
15
16
17
18
19
2
20
21
22
3
4
5
6
7
8
9
Do you have any other suggestions?
hyunminkang
commented
6 years ago I can't think of a reason why the likelihood would not be calculated when using all chromosomes while it works for chr1. I need to see some example file to be able to debug. I'm assuming both VCF and BAM files are indexed using tabix and samtools?
Thanks, Hyun.
On Wed, Apr 11, 2018 at 4:30 PM Harm Brugge notifications@github.com wrote:
Do you have any other suggestions?
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I'm trying to run demuxlet on reads generated by the 10x chromium pipeline. The bam files are generated using cellranger. On each lane we've pooled 6 individuals, so the input files (bam, vcf) contain the information of 6 indivuals. For the group-list argument we use the corrected barcode output file yielded by cellranger.
The complete command I'm using:
The software runs but the likelihoods in the generated output files are all set to 0. output_filtered_barcodes.best:
Error log:
Header and first 2 lines of the vcf file (this file is correctly sorted):
If i subset the VCF and BAM file for only chromosome 1 the likelihoods do seem to be correctly calculated:
Do you have any idea what might cause this issue