Hi everyone,

I am running the GATK somatic variant calling pipeline to find variants in tumor samples. GATK Variant Calling I followed the instructions and applied the CalculateContamination step including the output "tumor segmentation". I do not understand what the output means, it is a table that looks like this:

#<METADATA>SAMPLE=********
contig  start   end     minor_allele_fraction
NC_000021.9     46257034        46257034        0.4712756729842048
NC_000009.12    7170006 137185070       0.42814
NC_000012.12    25209843        111901211       0.4764214328637394
NC_000010.11    3138934 132224527       0.4
NC_000005.10    73051396        176888298       0.45671121453731034
NC_000013.11    24689401        24689401        0.4782817184520188
NC_000011.10    17641869        130120692       0.4824363044226485
NC_000006.12    38915166        131605194       0.47069194269498776
NC_000008.11    39473512        144084824       0.4483556651035815
NC_000014.9     19828351        104708748       0.47069194269498776
NC_000022.11    37886890        50150767        0.34266828397615634
NC_000019.10    7459969 58547326        0.48489773843072276
NC_000020.11    2317144 63312383        0.4764214328637394
NC_000018.10    9887939 9887939 0.4764214328637394
NC_000016.10    3549655 89546715        0.47069194269498776
NC_000017.11    4044239 51260896        0.4751054107038185
NC_000015.10    34225794        99139450        0.4786875830213102
NC_000004.12    888855  167234027       0.4727281546367458
NC_000007.14    2658247 158734189       0.3562305898749054
NC_000003.12    1383061 150565263       0.456008005764241
NC_000002.12    32465121        241126209       0.47178497924699475
NC_000001.11    3728190 201199371       0.4

Here is the command I used to generate it:

gatk CalculateContamination \
    -I tumor_pileups.table \
    -matched normal_pileups.table \
    -O contamination.table \
    -tumor-segmentation tumor_segments.table

What information does the table contain?

Thank you!

Best

Lynn