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== Getting Statistics from PGP1#21 and PGP1#22== * using flagstat to get statistics from combined bam file with the same method * In /media/NAS2_volume1/Eric/Eric_Syn15T/PGP1_21_BWA_MEM * In /media/NAS2_volume1/Eric/Eric_Syn15T/PGP1_22/BWA_MEM /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch01.sorted.bam > PGP1_21_ch01.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch02.sorted.bam > PGP1_21_ch02.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch03.sorted.bam > PGP1_21_ch03.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch04.sorted.bam > PGP1_21_ch04.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch05.sorted.bam > PGP1_21_ch05.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch06.sorted.bam > PGP1_21_ch06.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch07.sorted.bam > PGP1_21_ch07.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch08.sorted.bam > PGP1_21_ch08.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch09.sorted.bam > PGP1_21_ch09.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch10.sorted.bam > PGP1_21_ch10.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch11.sorted.bam > PGP1_21_ch11.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch12.sorted.bam > PGP1_21_ch12.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch13.sorted.bam > PGP1_21_ch13.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch14.sorted.bam > PGP1_21_ch14.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch15.sorted.bam > PGP1_21_ch15.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch16.sorted.bam > PGP1_21_ch16.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch17.sorted.bam > PGP1_21_ch17.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch18.sorted.bam > PGP1_21_ch18.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch19.sorted.bam > PGP1_21_ch19.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch20.sorted.bam > PGP1_21_ch20.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch21.sorted.bam > PGP1_21_ch21.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch22.sorted.bam > PGP1_21_ch22.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch23.sorted.bam > PGP1_21_ch23.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch24.sorted.bam > PGP1_21_ch24.sorted.bam.stat & cat *.stat > PGP1#21flagstatsorted.log /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch01.unique.bam > PGP1_21_ch01.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch02.unique.bam > PGP1_21_ch02.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch03.unique.bam > PGP1_21_ch03.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch04.unique.bam > PGP1_21_ch04.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch05.unique.bam > PGP1_21_ch05.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch06.unique.bam > PGP1_21_ch06.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch07.unique.bam > PGP1_21_ch07.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch08.unique.bam > PGP1_21_ch08.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch09.unique.bam > PGP1_21_ch09.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch10.unique.bam > PGP1_21_ch10.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch11.unique.bam > PGP1_21_ch11.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch12.unique.bam > PGP1_21_ch12.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch13.unique.bam > PGP1_21_ch13.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch14.unique.bam > PGP1_21_ch14.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch15.unique.bam > PGP1_21_ch15.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch16.unique.bam > PGP1_21_ch16.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch17.unique.bam > PGP1_21_ch17.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch18.unique.bam > PGP1_21_ch18.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch19.unique.bam > PGP1_21_ch19.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch20.unique.bam > PGP1_21_ch20.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch21.unique.bam > PGP1_21_ch21.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch22.unique.bam > PGP1_21_ch22.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch23.unique.bam > PGP1_21_ch23.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_21_ch24.unique.bam > PGP1_21_ch24.unique.bam.stat & cat *.stat2 > PGP1#21flagstatunique.log /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch01.sorted.bam > PGP1_22_ch01.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch02.sorted.bam > PGP1_22_ch02.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch03.sorted.bam > PGP1_22_ch03.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch04.sorted.bam > PGP1_22_ch04.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch05.sorted.bam > PGP1_22_ch05.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch06.sorted.bam > PGP1_22_ch06.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch07.sorted.bam > PGP1_22_ch07.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch08.sorted.bam > PGP1_22_ch08.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch09.sorted.bam > PGP1_22_ch09.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch10.sorted.bam > PGP1_22_ch10.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch11.sorted.bam > PGP1_22_ch11.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch12.sorted.bam > PGP1_22_ch12.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch13.sorted.bam > PGP1_22_ch13.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch14.sorted.bam > PGP1_22_ch14.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch15.sorted.bam > PGP1_22_ch15.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch16.sorted.bam > PGP1_22_ch16.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch17.sorted.bam > PGP1_22_ch17.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch18.sorted.bam > PGP1_22_ch18.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch19.sorted.bam > PGP1_22_ch19.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch20.sorted.bam > PGP1_22_ch20.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch21.sorted.bam > PGP1_22_ch21.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch22.sorted.bam > PGP1_22_ch22.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch23.sorted.bam > PGP1_22_ch23.sorted.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch24.sorted.bam > PGP1_22_ch24.sorted.bam.stat & cat *.stat > PGP1#22flagstatsorted.log /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch01.unique.bam > PGP1_22_ch01.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch02.unique.bam > PGP1_22_ch02.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch03.unique.bam > PGP1_22_ch03.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch04.unique.bam > PGP1_22_ch04.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch05.unique.bam > PGP1_22_ch05.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch06.unique.bam > PGP1_22_ch06.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch07.unique.bam > PGP1_22_ch07.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch08.unique.bam > PGP1_22_ch08.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch09.unique.bam > PGP1_22_ch09.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch10.unique.bam > PGP1_22_ch10.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch11.unique.bam > PGP1_22_ch11.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch12.unique.bam > PGP1_22_ch12.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch13.unique.bam > PGP1_22_ch13.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch14.unique.bam > PGP1_22_ch14.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch15.unique.bam > PGP1_22_ch15.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch16.unique.bam > PGP1_22_ch16.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch17.unique.bam > PGP1_22_ch17.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch18.unique.bam > PGP1_22_ch18.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch19.unique.bam > PGP1_22_ch19.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch20.unique.bam > PGP1_22_ch20.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch21.unique.bam > PGP1_22_ch21.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch22.unique.bam > PGP1_22_ch22.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch23.unique.bam > PGP1_22_ch23.unique.bam.stat & /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_22_ch24.unique.bam > PGP1_22_ch24.unique.bam.stat & cat *.stat2 > PGP1#22flagstatunique.log * unresolved haplotype 42727 1 0 chr4 44385955 A T 0/1 0 0.000000 0.000000 42728 1 0 chr4 44386866 C G 0/1 0 0.000000 0.000000 42729 1 0 chr4 44387711 A T 0/1 0 0.000000 0.000000 42730 0 1 chr4 44389586 C T 0/1 0 0.000000 0.000000 42731 1 0 chr4 44390186 C T 0/1 0 0.000000 0.000000 42732 1 0 chr4 44390791 T A 0/1 0 0.000000 0.000000 42733 0 1 chr4 44393140 G T 0/1 0 0.000000 0.000000 42737 - - chr4 44398478 T A 0/1 1 0.000000 -0.301025 42738 - - chr4 44398736 T G 0/1 1 0.000000 -0.301025 42739 - - chr4 44399022 T C 0/1 1 0.000000 -0.301025 42740 - - chr4 44399357 A G 0/1 1 0.000000 -0.301025 42741 - - chr4 44399962 A G 0/1 1 0.000000 -0.301025 42742 - - chr4 44400007 T A 0/1 1 0.000000 -0.301025 42743 - - chr4 44402567 G A 0/1 1 0.000000 -0.301025 42744 - - chr4 44403383 C A 0/1 1 0.000000 -0.301025 42745 1 0 chr4 44405423 C T 0/1 0 0.000000 0.000000 42747 1 0 chr4 44411910 G T 0/1 0 0.000000 0.000000 42748 0 1 chr4 44413222 C T 0/1 0 0.000000 0.000000 42749 1 0 chr4 44414209 C T 0/1 0 0.000000 0.000000 42750 1 0 chr4 44415512 G A 0/1 0 0.000000 0.000000 42751 0 1 chr4 44418391 C A 0/1 0 0.000000 0.000000 42752 0 1 chr4 44419764 G A 0/1 0 0.000000 0.000000 * it split chamber 14 in PGP1_21 instead of chamber 24
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