Structure of sex chromosomes in NGS data

depth-hist.py

# create a histogram of "samtools depth" outputs
# the output format is:
# #chr  <bin range of [start pos-end pos]>      <# of counted pos>      <total depth>
# bin size is fixed at 1Mb
import sys

def main():
        col_chr = 0
        col_pos = 1
        col_depth = 2
        bin_size = 1000000

        with sys.stdin as fin:
                current_chr = ""
                current_start_pos = 0
                current_end_pos = 0
                total_depth_in_bin = 0
                total_count_in_bin = 0
                for line in fin:
                        li = line.rstrip()
                        ls = li.split("\t")
                        chrm = ls[col_chr]
                        pos = int(ls[col_pos])
                        depth = int(ls[col_depth])
                        if chrm != current_chr: # chr updated
                                if current_start_pos != 0:
                                        print "%s\t%d-%d\t%d\t%d" %(current_chr, current_start_pos, current_end_pos, total_count_in_bin, total_depth_in_bin)
                                current_chr = chrm
                                current_start_pos = pos
                                total_depth_in_bin = depth
                                total_count_in_bin = 1
                                continue
                        if pos - current_start_pos + 1 > bin_size: # a bin is full
                                print "%s\t%d-%d\t%d\t%d" %(current_chr, current_start_pos, current_end_pos, total_count_in_bin, total_depth_in_bin)
                                current_start_pos = pos
                                total_depth_in_bin = depth
                                total_count_in_bin = 1
                                continue
                        total_depth_in_bin = total_depth_in_bin + depth
                        total_count_in_bin = total_count_in_bin + 1
                        current_end_pos = pos
                #end of file
                print "%s\t%d-%d\t%d\t%d" %(current_chr, current_start_pos, current_end_pos, total_count_in_bin, total_depth_in_bin)
        return 0

if __name__ == '__main__':
        main()

bin size = 1Mb

$ samtools depth -a DRR028634.bam | python ~/depth-hist.py > DRR028634.bam.depth.hist &

DRR028634.bam.depth.hist

♀ (XX), but it has an abnormal structure (X + X fragment)

♀ (XX)

♂ (XY)

♂ (XY)

Other chromosomal aberrations in NGS data

Trisomy 8

Trisomy is detected in GLS1 cells.