[Samtools-help] Help in calling indel

[Fox, Dylan]

Hi,

I am trying to call substitutions and indels in with samtools / bcftools (versions 1.3.1 / 1.3.1-209-g1618245), and I am unable to call an indel that is in the bam. Looking at the bam in a viewer confirms that there is an indel at chr7 position 117559590 that deletes a TCT sequence. Following the instructions on http://www.htslib.org/workflow/#mapping_to_variant, I used a similar pipeline on the indexed bam:

samtools mpileup -x -d 1000000 -B -ugf <ref.fa> <sample.bam> | bcftools call -vmO z -o <study.vcf.gz>

I added flags parameters -x, -d, -B because they seem relevant to this data, and adding them do not seem to cause this issue I'm having.
Upon viewing the vcf, there does not appear to be any snp called at chr7 position 117559590:
...
"
chr7 117541810 . G T 11.4963 . DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=40 GT:PL 0/1:39,3,0
chr7 117541812 . G T 10.5754 . DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=40 GT:PL 0/1:38,3,0
chr7 117541813 . A G 11.4963 . DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=40 GT:PL 0/1:39,3,0
chr7 117548628 . G T 210 . DP=2032;VDB=0;SGB=-0.693147;RPB=0.925993;MQB=0;MQSB=0.9998;BQB=8.21384e-07;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=496,497,520,519;MQ=28 GT:PL 0/1:243,0,255
chr7 117559403 . A G 200 . DP=344;VDB=0;SGB=-0.693147;RPB=0.995508;MQB=0.958341;BQB=0.736929;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=175,0,169,0;MQ=41 GT:PL
0/1:233,0,224
chr7 117559479 . G A 222 . DP=694;VDB=0;SGB=-0.693147;RPB=6.85819e06;MQB=0.95608;MQSB=1;BQB=0.986478;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=180,179,167,168;MQ
=41 GT:PL 0/1:255,0,255
"
*** SHOULD BE HERE ***
"
chr7 117587989 . T C 11.4963 . DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=40 GT:PL 0/1:39,3,0
chr7 117587995 . T A 11.4963 . DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=40 GT:PL 0/1:39,3,0
chr7 117587997 . A G 11.4963 . DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=40 GT:PL 0/1:39,3,0
chr7 117587999 . G T 11.4963 . DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=40 GT:PL 0/1:39,3,0
"
...
I then used mpileup to generate a pileup file so I could confirm whether mpileup was recognizing the snp. I used:

samtools mpileup -x -d 1000000 -B -f <ref.fa> -o <test.pileup> <sample.bam>

This yielded this output at the region of interest:
"
chr7 117559590 A 3686 .$..-3TCT..$.$.$.,-3tct,,-3tct,-3tct,,,,,,,,,-3tct,,,,,-3tct,-3tct,,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,g,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,-3tct.-3TCT....-3TCT.-3TCT..-3TCT..-3TCT..-3TCT.-3TCT...-3TCT..-3TCT.-3TCT.....-3TCT......-3TCT.-3TCT.-3TCT..-3TCT..-3TCT..-3TCT..-3TCT.-3TCT.-3TCT.-3TCT..-3TCT..-3TCT....-3TCT....-3TCT.....-3TCT.-3TCT.....-3TCT...-3TCT..-3TCT.......-3TCT.-3TCT.-3TCT.-3TCT.-3TCT.-3TCT..-3TCT.-3TCT..-3TCT.-3TCT.-3TCT.-3TCT...-3TCT..-3TCT.....-3TCT.-3TCT.-3TCT.-3TCT.-3TCT...-3TCT.-3TCT.....-3TCT.-3TCT...-3TCT...-3TCT..-3TCT.-3TCT.-3TCT.-3TCT...-3TCT...-3TCT..-3TCT.-3TCT.-3TCT.-3TCT..-3TCT..-3TCT...-3TCT.......-3TCT...-3TCT.....-3TCT......-3TCT.-3TCT.....-3TCT.-3TCT..-3TCT.-3TCT...-3TCT..-3TCT..-3TCT......-3TCT.-3TCT.-3TCT.-3TCT.-3TCT...-3TCT..-3TCT.-3TCT..-3TCT.-3TCT..-3TCT.-3TCT.-3TCT.-3TCT...-3TCT..-3TCT.-3TCT..-3TCT..-3TCT.-3TCT.-3TCT.-3TCT..-3TCT.
"
...
"
HHHHH<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
"

This pileup data is consistent with the bam viewer I used, yet somehow there is a disconnect in calling the indel in the final vcf. Hopefully I'm just missing a flag or parameter. Any thoughts on why I am not able to call this snp? Any help will be greatly appreciated!
Thanks,
-dylan

[Petr Danecek]

Hi Dylan,

check if the mpileup --gap-frac or --min-ireads options are perhaps
causing it? Otherwise it is hard to tell without actually seeing the
data.

Petr

Post by Fox, Dylan
Hi,
 
I am trying to call substitutions and indels in with samtools /
bcftools (versions 1.3.1 / 1.3.1-209-g1618245), and I am unable to
call an indel that is in the bam. Looking at the bam in a viewer
confirms that there is an indel at chr7 position 117559590 that
deletes a TCT sequence. Following the instructions on http://www.htsl
ib.org/workflow/#mapping_to_variant, I used a similar pipeline on the
samtools mpileup -x -d 1000000 -B -ugf <ref.fa> <sample.bam> |
bcftools call -vmO z -o <study.vcf.gz>
 
I added flags parameters -x, -d, -B because they seem relevant to
this data, and adding them do not seem to cause this issue I’m
having.
Upon viewing the vcf, there does not appear to be any snp called at
…
“
chr7    117541810       .       G       T       11.4963 .      
DP=1;SGB=-
0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=40     GT:PL  
0/1:39,3,0
chr7    117541812       .       G       T       10.5754 .    
  DP=1;SGB=-
0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=40     GT:PL  
0/1:38,3,0
chr7    117541813       .       A       G       11.4963 .      
DP=1;SGB=-
0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=40     GT:PL  
0/1:39,3,0
chr7    117548628       .       G       T       210     .      
DP=2032;VDB=0;SGB=-
0.693147;RPB=0.925993;MQB=0;MQSB=0.9998;BQB=8.21384e-
07;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=496,497,520,519;MQ=28    
GT:PL   0/1:243,0,255
chr7    117559403       .       A       G       200     .      
DP=344;VDB=0;SGB=-
0.693147;RPB=0.995508;MQB=0.958341;BQB=0.736929;MQ0F=0;ICB=1;HOB=0.5;
AC=1;AN=2;DP4=175,0,169,0;MQ=41 GT:PL
0/1:233,0,224
chr7    117559479       .       G       A       222     .      
DP=694;VDB=0;SGB=-
0.693147;RPB=6.85819e06;MQB=0.95608;MQSB=1;BQB=0.986478;MQ0F=0;ICB=1;
HOB=0.5;AC=1;AN=2;DP4=180,179,167,168;MQ
=41     GT:PL   0/1:255,0,255
“
*** SHOULD BE HERE ***
“
chr7    117587989       .       T       C       11.4963 .      
DP=1;SGB=-
0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=40     GT:PL  
0/1:39,3,0
chr7    117587995       .       T       A       11.4963 .      
DP=1;SGB=-
0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=40     GT:PL  
0/1:39,3,0
chr7    117587997       .       A       G       11.4963 .      
DP=1;SGB=-
0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=40     GT:PL  
0/1:39,3,0
chr7    117587999       .       G       T       11.4963 .      
DP=1;SGB=-
0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=40     GT:PL  
0/1:39,3,0
“
…
I then used mpileup to generate a pileup file so I could confirm
whether mpileup was recognizing the snp. I used: 
samtools mpileup -x -d 1000000 -B -f <ref.fa> -o <test.pileup>
<sample.bam>
“
chr7    117559590       A       3686    .$..-3TCT..$.$.$.,-3tct,,-
3tct,-3tct,,,,,,,,,-3tct,,,,,-3tct,-3tct,,-3tct,-3tct,-3tct,-3tct,-
3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-
3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-
3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-
3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-
3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-
3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-
3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-
3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-
3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-
3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-
3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,,-
3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-
3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-
3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-
3tct,-3tct,-
3tct,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
,,,,,,,,,,,,,,,,,,g,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,-3tct.-3TCT....-3TCT.-3TCT..-3TCT..-
3TCT..-3TCT.-3TCT...-3TCT..-3TCT.-3TCT.....-3TCT......-3TCT.-3TCT.-
3TCT..-3TCT..-3TCT..-3TCT..-3TCT.-3TCT.-3TCT.-3TCT..-3TCT..-3TCT....-
3TCT....-3TCT.....-3TCT.-3TCT.....-3TCT...-3TCT..-3TCT.......-3TCT.-
3TCT.-3TCT.-3TCT.-3TCT.-3TCT..-3TCT.-3TCT..-3TCT.-3TCT.-3TCT.-
3TCT...-3TCT..-3TCT.....-3TCT.-3TCT.-3TCT.-3TCT.-3TCT...-3TCT.-
3TCT.....-3TCT.-3TCT...-3TCT...-3TCT..-3TCT.-3TCT.-3TCT.-3TCT...-
3TCT...-3TCT..-3TCT.-3TCT.-3TCT.-3TCT..-3TCT..-3TCT...-3TCT.......-
3TCT...-3TCT.....-3TCT......-3TCT.-3TCT.....-3TCT.-3TCT..-3TCT.-
3TCT...-3TCT..-3TCT..-3TCT......-3TCT.-3TCT.-3TCT.-3TCT.-3TCT...-
3TCT..-3TCT.-3TCT..-3TCT.-3TCT..-3TCT.-3TCT.-3TCT.-3TCT...-3TCT..-
3TCT.-3TCT..-3TCT..-3TCT.-3TCT.-3TCT.-3TCT..-3TCT.
”
…  
“
HHHHH<HHH3HHHHHHHHFGHHH1HHFHH1HHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFHH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“
This pileup data is consistent with the bam viewer I used, yet
somehow there is a disconnect in calling the indel in the final vcf.
Hopefully I’m just missing a flag or parameter. Any thoughts on why I
am not able to call this snp? Any help will be greatly appreciated!
Thanks,
-dylan
 
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