Sequenza.extract ERROR

[Tusharika Rastogi]

Hello,

I am trying to use the sequenza.extract function to process the seqz data. I produced the seqz data using the snp2seqz function of sequenza package. But I run into the following error:

> test <- sequenza.extract("/home/sequenza/sample_bin50.seqz.gz", verbose=TRUE)

Collecting GC information . done

Processing chr1:

Error in data.frame(base.count = as.integer(n.base.mut), maj.base.freq = as.numeric(max.freqs[,  : 

  arguments imply differing number of rows: 35, 31

In addition: There were 50 or more warnings (use warnings() to see the first 50)

I have tried both the seqz files - before binning and after binning - but the error persists. Here is a snapshot of the seqz file for your reference.

Before binning:

zcat < sample.seqz.gz | head

chromosome position base.ref depth.normal depth.tumor depth.ratio Af Bf zygosity.normal GC.percent good.reads AB.normal AB.tumor tumor.strand

chr1 183685 T 43 107 2.488 0.72 0 hom 60 107 T . 0

chr1 873743 G 152 567 3.73 0.984 0 hom 68 567 G . 0

chr1 873755 C 161 590 3.665 0.973 0 hom 64 590 C . 0

chr1 873966 CA 68 303 4.456 0.964 0 hom 60 303 CA . 0

chr1 962487 G 56 171 3.054 0.977 0 hom 78 171 G A0.023 A0.0

chr1 1046480 G 89 278 3.124 0.96 0 hom 82 278 G . 0

chr1 1091417 G 56 268 4.786 0.985 0 hom 72 268 G A0.015 A0.0

chr1 1212596 AC 45 114 2.533 0.877 0 hom 72 114 AC . 0

chr1 1213131 G 183 526 2.874 0.989 0 hom 74 526 G A0.011 A0.0

zcat < sample.seqz.gz | tail

chrY 10191824 T 44 188 4.273 0.979 0 hom 32 188 T C0.021 C0.0

chrY 12833900 G 19 77 4.053 0.922 0 hom 34 77 G . 0

chrY 12837845 TA 9 45 5.0 0.846 0 hom 44 39 TA T0.154 T0.0

chrY 18992661 CCAG 83 338 4.072 0.988 0 hom 68 338 CCAG . 0

chrY 19732747 CAA 16 60 3.75 0.851 0 hom 42 47 CAA C0.149 C0.0

chrY 26634537 A 19 98 5.158 0.939 0 hom 50 98 A G0.061 G0.0

chrY 56855242 AAAG 97 384 3.959 0.883 0 hom 14 384 AAAG . 0

chrY 56855316 C 512 1522 2.973 0.995 0 hom 58 1522 C . 0

chrY 56855330 C 597 1675 2.806 0.99 0 hom 58 1675 C . 0

chrY 56855530 C 226 787 3.482 0.909 0 hom 34 787 C . 0

After binning:

zcat < sample_bin50.seqz.gz | head

chromosome position base.ref depth.normal depth.tumor depth.ratio Af Bf zygosity.normal GC.percent good.reads AB.normal AB.tumor tumor.strand

chr1 183685 N 43 107 2.488 1.0 0 hom 60 1 N . 0

chr1 873743 N 156 578 3.697 1.0 0 hom 66 2 N . 0

chr1 873966 N 68 303 4.456 1.0 0 hom 60 1 N . 0

chr1 962487 G 56 171 3.054 0.977 0 hom 60 171 G A0.023 A0.0

chr1 962487 N 56 171 3.054 1.0 0 hom 78 1 N . 0

chr1 1046480 N 89 278 3.124 1.0 0 hom 82 1 N . 0

chr1 1091417 G 56 268 4.786 0.985 0 hom 82 268 G A0.015 A0.0

chr1 1091417 N 56 268 4.786 1.0 0 hom 72 1 N . 0

chr1 1212596 N 45 114 2.533 1.0 0 hom 72 1 N . 0

zcat < sample_bin50.seqz.gz | tail

chrY 12837845 TA 9 45 5.0 0.846 0 hom 34 39 TA T0.154 T0.0

chrY 12837845 N 9 45 5.0 1.0 0 hom 44 1 N . 0

chrY 18992661 N 83 338 4.072 1.0 0 hom 68 1 N . 0

chrY 19732747 CAA 16 60 3.75 0.851 0 hom 68 47 CAA C0.149 C0.0

chrY 19732747 N 16 60 3.75 1.0 0 hom 42 1 N . 0

chrY 26634537 A 19 98 5.158 0.939 0 hom 42 98 A G0.061 G0.0

chrY 26634537 N 19 98 5.158 1.0 0 hom 50 1 N . 0

chrY 56855242 N 97 384 3.959 1.0 0 hom 14 1 N . 0

chrY 56855316 N 554 1598 2.889 1.0 0 hom 58 2 N . 0

chrY 56855530 N 226 787 3.482 1.0 0 hom 34 1 N . 0

Please let me know what can I do to fix this. Thank you so much.

Best,

Tusharika