Question: Error in qaVariants() in package " VariantTools"
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gravatar for jd841029
4.4 years ago by
jd8410290
Australia
jd8410290 wrote:

Dear All, I am trying to analyze genome data using "gmapR" and "VariantTools".

I get the below error when using qaVariants( ) function.

> tallies <- tallyVariants("1.bam", param, BPPARAM = bpp)    

> qa.variants <- qaVariants(tallies)

Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘softFilterMatrix’ for signature ‘"list"’

> vcf <- asVCF(tallies)

Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘asVCF’ for signature ‘"list"’

And the head of tallies derived from tallyVariants( )  is:

> head(tallies)

$message
[1] "sequences 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y have incompatible seqlengths:\n  - in 'x': 248956422, 242193529, 198295559, 190214555, 181538259, 170805979, 159345973, 145138636, 138394717, 133797422, 135086622, 133275309, 114364328, 107043718, 101991189, 90338345, 83257441, 80373285, 58617616, 64444167, 46709983, 50818468, 156040895, 57227415\n  - in 'y': 249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566"

$call
mergeNamedAtomicVectors(seqlengths(x), seqlengths(y), what = c("sequence",
    "seqlengths"))

$message
[1] "sequences 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y have incompatible seqlengths:\n  - in 'x': 248956422, 242193529, 198295559, 190214555, 181538259, 170805979, 159345973, 145138636, 138394717, 133797422, 135086622, 133275309, 114364328, 107043718, 101991189, 90338345, 83257441, 80373285, 58617616, 64444167, 46709983, 50818468, 156040895, 57227415\n  - in 'y': 249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566"

$call
mergeNamedAtomicVectors(seqlengths(x), seqlengths(y), what = c("sequence",
    "seqlengths"))

$message
[1] "sequences 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y have incompatible seqlengths:\n  - in 'x': 248956422, 242193529, 198295559, 190214555, 181538259, 170805979, 159345973, 145138636, 138394717, 133797422, 135086622, 133275309, 114364328, 107043718, 101991189, 90338345, 83257441, 80373285, 58617616, 64444167, 46709983, 50818468, 156040895, 57227415\n  - in 'y': 249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566"

$call
mergeNamedAtomicVectors(seqlengths(x), seqlengths(y), what = c("sequence",
    "seqlengths"))

 

Thanks in advance for your help.

Regards,

kangyang

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