alignment view and vcf disagree

Mark · 09-28-2020, 06:53 AM

I have a pacbio CCS fastq file that I have aligned to a small (5037 bp) reference which is part of a sequenced BAC clone. I have aligned this data with multiple aligners (minimap2 and smalt), called variants with multiple variant callers (bbmap, freebayes, and gatk) and viewed the bam file with multiple viewers (igv and tablet). All produce similar results. I will focus here on minimap2 and callvariants (bbmap), as the problem likely stems from the variant caller and seqanswers is the preferred avenue for support for bbmap.
Here is what I did:

Code:

minimap2 -t 5 -ax asm20 reference.fa  sample.ccs.fastq > out.sam
samtools view -O BAM -o out.bam out.sam && samtools sort -o out.sort.bam out.bam && samtools index out.sort.bam
callvariants.sh ploidy=1 in=out.sort.bam ref=reference.fa vcf=out.vcf

A partial reading of callvariants log output:

Code:

1 of 3311 variants passed primary filters (0.0302%).
Type            Count   Rate    AD      Depth   AF      Score   Qual
Substitutions:  0       0.0%    0.0     0.0     0.000   0.0     0.0
Deletions:      1       100.0%  619.0   1000.0  0.619   23.0    34.0
Insertions:     0       0.0%    0.0     0.0     0.000   0.0     0.0
Variation Rate: 1/5037
Homozygous:     1       100.0%

The single called variant (a deletion at the site of a homopolymer) is reported in the vcf.

Code:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  out.sort
reference       1401    .       Tc      T       23.66   PASS    SN=0;STA=1401;STO=1402;TYP=DEL;R1P=338;R1M=281;R2P=0;R2M=0;AD=619;DP=1000;MCOV=-1;PPC=0;AF=0.6190;RAF=0.6190;LS=2996497;MQS=37140;MQM=60;BQS=21455;BQM=41;EDS=956749;EDM=4467;IDS=617766;IDM=999;NVC=0;FLG=0;CED=601;HMP=6;SB=0.9997    GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF        1:1000:619:0.6190:0.6190:0:0:0.9997:23.66:PASS

To my interpretation of this, a single "c" has been lost from the poly-C which starts at this position. Moreover this deletions occurs in 619 of 1000 reads covering this position.
Now the strange part. When I view the alignment (out.sort.bam) in IGV (or Tablet), I see at most 1-2% indels at our near this site while the rest of the sequence is largely free of indels. Why is there this large discrepancy between what is observed in an alignment viewer and what is called by the variant caller (i.e. there are many more variant reads called than are observed on the viewer?

Thank you for your help

Mark · 09-29-2020, 09:02 AM

Turns out the problem was, not surprisingly, in IGV. By default IGV will not show one base pair deletions for what it perceives as PacBio sequence. I had unchecked the "hide indels" box in the 'alignment' preferences but there is a equivalent checkbox in the ' Third Gen' preferences I had overlooked. Uncheck it and viola.

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09-28-2020, 06:53 AM	#1
Mark Member Location: Raleigh, NC Join Date: Nov 2008 Posts: 51	alignment view and vcf disagree I have a pacbio CCS fastq file that I have aligned to a small (5037 bp) reference which is part of a sequenced BAC clone. I have aligned this data with multiple aligners (minimap2 and smalt), called variants with multiple variant callers (bbmap, freebayes, and gatk) and viewed the bam file with multiple viewers (igv and tablet). All produce similar results. I will focus here on minimap2 and callvariants (bbmap), as the problem likely stems from the variant caller and seqanswers is the preferred avenue for support for bbmap. Here is what I did: Code: minimap2 -t 5 -ax asm20 reference.fa sample.ccs.fastq > out.sam samtools view -O BAM -o out.bam out.sam && samtools sort -o out.sort.bam out.bam && samtools index out.sort.bam callvariants.sh ploidy=1 in=out.sort.bam ref=reference.fa vcf=out.vcf A partial reading of callvariants log output: Code: 1 of 3311 variants passed primary filters (0.0302%). Type Count Rate AD Depth AF Score Qual Substitutions: 0 0.0% 0.0 0.0 0.000 0.0 0.0 Deletions: 1 100.0% 619.0 1000.0 0.619 23.0 34.0 Insertions: 0 0.0% 0.0 0.0 0.000 0.0 0.0 Variation Rate: 1/5037 Homozygous: 1 100.0% The single called variant (a deletion at the site of a homopolymer) is reported in the vcf. Code: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT out.sort reference 1401 . Tc T 23.66 PASS SN=0;STA=1401;STO=1402;TYP=DEL;R1P=338;R1M=281;R2P=0;R2M=0;AD=619;DP=1000;MCOV=-1;PPC=0;AF=0.6190;RAF=0.6190;LS=2996497;MQS=37140;MQM=60;BQS=21455;BQM=41;EDS=956749;EDM=4467;IDS=617766;IDM=999;NVC=0;FLG=0;CED=601;HMP=6;SB=0.9997 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1:1000:619:0.6190:0.6190:0:0:0.9997:23.66:PASS To my interpretation of this, a single "c" has been lost from the poly-C which starts at this position. Moreover this deletions occurs in 619 of 1000 reads covering this position. Now the strange part. When I view the alignment (out.sort.bam) in IGV (or Tablet), I see at most 1-2% indels at our near this site while the rest of the sequence is largely free of indels. Why is there this large discrepancy between what is observed in an alignment viewer and what is called by the variant caller (i.e. there are many more variant reads called than are observed on the viewer? Thank you for your help Last edited by Mark; 09-28-2020 at 12:37 PM. Reason: Added [code] tags

09-29-2020, 09:02 AM	#2
Mark Member Location: Raleigh, NC Join Date: Nov 2008 Posts: 51	Turns out the problem was, not surprisingly, in IGV. By default IGV will not show one base pair deletions for what it perceives as PacBio sequence. I had unchecked the "hide indels" box in the 'alignment' preferences but there is a equivalent checkbox in the ' Third Gen' preferences I had overlooked. Uncheck it and viola.