variant calling chromosome-wise from WGS data

Question

[analyst]

I have aneuploid sugarcane WGS data. I am using hybrid reference genome R570 with following genomic architecture as a reference for alignment:

Chr10A
Chr10B
Chr10C
Chr10D
Chr10E
Chr10F
Chr10os1
Chr10os2
Chr10os3
Chr1A
Chr1B
Chr1C
Chr1D
Chr1E
Chr1F
Chr1os1
Chr1os2
Chr1os3
Chr1os4
Chr1os5
Chr2A
Chr2B
Chr2C
Chr2D
Chr2E
Chr2F
Chr2G
Chr2os1
Chr3A
Chr3B
Chr3C
Chr3D
Chr3E
Chr3F
Chr3G
Chr3os1
Chr3os2
Chr3os3
Chr3os4
Chr3os5
Chr4A
Chr4B
Chr4C
Chr4D
Chr4E
Chr4F
Chr4G
Chr4os1
Chr5_9A
Chr5A
Chr5B
Chr5C
Chr5D
Chr5E
Chr5F
Chr5G
Chr5os1
Chr5os2
Chr6_9A
Chr6A
Chr6B
Chr6C
Chr6D
Chr6E
Chr6F
Chr6G
Chr6os1
Chr7_10A
Chr7A
Chr7B
Chr7C
Chr7D
Chr7E
Chr7os1
Chr8_10A
Chr8_5A
Chr8A
Chr8B
Chr8C
Chr8D
Chr8E
Chr9A
Chr9B
Chr9C
Chr9D
Chr9E
Chr9os1
scaffold_100
scaffold_101
scaffold_102
scaffold_103
scaffold_104
scaffold_105
scaffold_106
scaffold_107
scaffold_108
scaffold_109
scaffold_110
scaffold_111
scaffold_112
scaffold_113
scaffold_114
scaffold_115
scaffold_116
scaffold_117
scaffold_118
scaffold_119
scaffold_120
scaffold_121
scaffold_122
scaffold_123
scaffold_124
scaffold_125
scaffold_126
scaffold_127
scaffold_128
scaffold_129
scaffold_130
scaffold_131
scaffold_132
scaffold_133
scaffold_134
scaffold_135
scaffold_136
scaffold_137
scaffold_138
scaffold_139
scaffold_140
scaffold_141
scaffold_142
scaffold_143
scaffold_144
scaffold_88
scaffold_89
scaffold_90
scaffold_91
scaffold_92
scaffold_93
scaffold_94
scaffold_95
scaffold_96
scaffold_97
scaffold_99

Since deduplicated bam file is large in size due to 100x coverage so I split my bam file according to chromosomes given above. Now I am confused to set ploidy for each bam file named as list above. Please provide you valuable suggestion how to determine ploidy level through above provided chromosome information.

[cmdcolin]

I'm not experienced with this type of problem, but you may be able to get some coarse-level understanding of the plody by just looking at average the read depth across your aligned BAM file. "samtools coverage yourfile.bam" can output this info

[GenoMax]

Based on some recent posts from OP this is (as long as it is the same data) for an aneuploid plant with polyploidy ranging widely from 8 to 12, so a simple samtools coverage may not be sufficient. A prior post to that effect was deleted by OP since it did not generate any responses.

[analyst]

What do you suggest should i use ploidy 12 for each chromosomes for variant calling? Or using coverage information provided below can I determine ploidy level.

Your guidance is highly appreciated!

[analyst]

**Chromosome    Avg_Coverage**
Chr10A.bam  55.49
Chr10B.bam  47.28
Chr10C.bam  46.83
Chr10D.bam  52.52
Chr10E.bam  38.16
Chr10F.bam  56.22
Chr10os1.bam    42.29
Chr10os2.bam    43.31
Chr10os3.bam    38.87
Chr1A.bam   67.36
Chr1B.bam   72.88
Chr1C.bam   79.07
Chr1D.bam   60.93
Chr1E.bam   62.16
Chr1F.bam   51.1
Chr1os1.bam 101.61
Chr1os2.bam 64.33
Chr1os3.bam 61.35
Chr1os4.bam 91.46
Chr1os5.bam 93.83
Chr2A.bam   57.32
Chr2B.bam   78.16
Chr2C.bam   60.28
Chr2D.bam   51.91
Chr2E.bam   47.08
Chr2F.bam   62.48
Chr2G.bam   52.41
Chr2os1.bam 74.32
Chr3A.bam   84.95
Chr3B.bam   56.18
Chr3C.bam   75.49
Chr3D.bam   63.25
Chr3E.bam   54.92
Chr3F.bam   53.26
Chr3G.bam   60.62
Chr3os1.bam 69.57
Chr3os2.bam 29.51
Chr3os3.bam 39.32
Chr3os4.bam 50.34
Chr3os5.bam 42.74
Chr4A.bam   73.12
Chr4B.bam   42.05
Chr4C.bam   37.17
Chr4D.bam   62.88
Chr4E.bam   64.87
Chr4F.bam   57.69
Chr4G.bam   53.15
Chr4os1.bam 60.76
Chr5_9A.bam 41.8
Chr5A.bam   37.92
Chr5B.bam   61.11
Chr5C.bam   74.17
Chr5D.bam   52.43
Chr5E.bam   61.17
Chr5F.bam   49.69
Chr5G.bam   77.64
Chr5os1.bam 40.62
Chr5os2.bam 83.1
Chr6_9A.bam 46.57
Chr6A.bam   61.5
Chr6B.bam   89.58
Chr6C.bam   51.27
Chr6D.bam   112.9
Chr6E.bam   58.47
Chr6F.bam   65.61
Chr6G.bam   51.15
Chr6os1.bam 60.75
Chr7_10A.bam    48.05
Chr7A.bam   68.64
Chr7B.bam   62.02
Chr7C.bam   48.01
Chr7D.bam   56.32
Chr7E.bam   78.58
Chr7os1.bam 56.21
Chr8_10A.bam    69.92
Chr8_5A.bam 70.74
Chr8A.bam   73.13
Chr8B.bam   64.74
Chr8C.bam   44.16
Chr8D.bam   53.59
Chr8E.bam   78.76
Chr9A.bam   55.69
Chr9B.bam   69.3
Chr9C.bam   58.01
Chr9D.bam   59.95
Chr9E.bam   49.31
Chr9os1.bam 57.19
scaffold_100.bam    51.85
scaffold_101.bam    67.26
scaffold_102.bam    44.33
scaffold_103.bam    44.04
scaffold_104.bam    32.59
scaffold_105.bam    63.54
scaffold_106.bam    58.96
scaffold_107.bam    74.19
scaffold_108.bam    55.52
scaffold_109.bam    64.77
scaffold_110.bam    58.59
scaffold_111.bam    41.37
scaffold_112.bam    41.98
scaffold_113.bam    43.41
scaffold_114.bam    33.87
scaffold_115.bam    74.85
scaffold_116.bam    48.1
scaffold_117.bam    79.52
scaffold_118.bam    135.01
scaffold_119.bam    195.39
scaffold_120.bam    23.32
scaffold_121.bam    45.25
scaffold_122.bam    49.43
scaffold_123.bam    80.88
scaffold_124.bam    39.77
scaffold_125.bam    77.94
scaffold_126.bam    111.95
scaffold_127.bam    105.44
scaffold_128.bam    67.16
scaffold_129.bam    37.74
scaffold_130.bam    81.4
scaffold_131.bam    38.17
scaffold_132.bam    71.61
scaffold_133.bam    90.85
scaffold_134.bam    114.36
scaffold_135.bam    101.42
scaffold_136.bam    82.03
scaffold_137.bam    68.78
scaffold_138.bam    46.26
scaffold_139.bam    50.31
scaffold_140.bam    63.41
scaffold_141.bam    71.34
scaffold_142.bam    105.61
scaffold_143.bam    37.6
scaffold_144.bam    48.35
scaffold_88.bam 47.93
scaffold_89.bam 35.72
scaffold_90.bam 29.64
scaffold_91.bam 37.7
scaffold_92.bam 38.16
scaffold_93.bam 29.36
scaffold_94.bam 44.88
scaffold_95.bam 66.4
scaffold_96.bam 101.9
scaffold_97.bam 28.58
scaffold_99.bam 4.03